[R] Why daisy() in cluster library failed to exclude NA when computing dissimilarity

Hi, According to daisy function from cluster documentation, it can compute dissimilarity when NA (missing) value(s) is present. http://stat.ethz.ch/R-manual/R-devel/library/cluster/html/daisy.html But why when I tried this code library(cluster) x <- c(1.115,NA,NA,0.971,NA) y <- c(NA,1.006,NA,N

[R] How to perform clustering without removing rows where NA is present in R

I have a data which contain some NA value in their elements. What I want to do is to **perform clustering without removing rows** where the NA is present. I understand that `gower` distance measure in `daisy` allow such situation. But why my code below doesn't work? __BEGIN__ # plot heat map

[R] Interpreting the result of 'cutree' from hclust/heatmap.2

I have the following code that perform hiearchical clustering and plot them in heatmap. __ library(gplots) set.seed(538) # generate data y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep=""))) # the actual data is much larger that the above # perform hiear

[R] Replacing part of delimited string with R's regex

I have the following list of strings: name <- c("hsa-miR-555p","hsa-miR-519b-3p","hsa-let-7a") What I want to do is for each of the above strings replace the text after second delimiter with "zzz". Yielding: hsa-miR-zzz hsa-miR-zzz hsa-let-zzz What's the way to do it? [[alternative HTM

[R] How to include ifelse condition to adjust QPLOT font size

I have a data which I plot using this code. Attached is the plot _BEGIN_ library(ggplot2) dat.m <- read.delim("http://dpaste.com/1269939/plain/",sep="";) colnames(dat.m) <- c("ensg","mirna_hgc","variable","value") dat.m.y <- subset(dat.m,dat.m$variable=="y") qplot(value,data=dat.m.y, geom="bar",

[R] How to expand.grid with string elements (the half!)

I have the following result of expand grid: > d <- expand.grid(c("x","y","z"),c("x","y","z")) What I want is to create a combination of strings but only the half of the all combinations: Var1 Var2 1xx 2yx 3 yy 4 zy 5 xz 6zz What's the way to do it?

[R] All against all correlation matrix with GGPLOT Facet

I have the following data: v <- rnorm(13) w <- rnorm(13) x <- rnorm(13) y <- rnorm(13) z <- rnorm(13) Using GGPLOT facet, what I want to do is to create a 5*5 matrix, where each cells plot the correlation between each pair of the above data. E.g. v-v,v-w; v-x,...,z-z What's the way to do it? A

[R] Choice of statistical test (in R) of two apparently different distributions

I have the following list of data each has 10 samples. The values indicate binding strength of a particular molecule. What I want so show is that 'x' is statistically different from 'y', 'z' and 'w'. Which it does if you look at X it has more values greater than zero (2.8,1.00,5.4, etc) than othe

[R] Standard Error and P-Value from cor()

Is there a native way to produce SE of correlation in R's cor() functions and p-value from T-test? As explained in this web http://www.sjsu.edu/faculty/gerstman/StatPrimer/correlation.pdf (page 14.6) The standard error is sqrt((1-r^2)/(n-2)), where n- is the number of sample. - G.V. [[

[R] How to remove all characters after comma in R

I have the following list of strings: x <- c("foo, foo2, foo3", "bar", "qux, qux1") what I want to do is to obtain foo, bar qux Namely for each element in the vector obtain only string before the first comma. What's the way to do it? - G.V. [[alternative HTML version deleted]] _

[R] Transforming 4x3 data frame into 2 column df in R

I have the following data frame: > foo w x y z n 1.51550092 1.4337572 1.2791624 1.1771230 q 0.09977303 0.8173761 1.6123402 0.1510737 r 1.17083866 1.2469347 0.8712135 0.8488029 What I want to do is to change it into : > newdf 1 nw 1.51550092 2 q w

[R] Best way to plot normalization in R

I have a data that looks like this: mRNA Value --- mRNA1 30 mRNA2 199 ...... ... mRNA1000 13 Then I'll normalize the value based on the s

[R] R package for normalizing microarray with few samples

I have only *two* datasets from normal and cancer samples. CancerNormal -- mRNA1 3049 mRNA2 199200 ... ... ... mRNA1000 1340 Each samples contain several thousan mRNA microarray express

[R] How to use the value of "rect" to determine the location of legend

Given the attached plot, how can I locate the center text with "Mean and SD" so that it can be placed exactly under "---emp".? The current code I have is this: L = list(bquote(Em.Mean ==.(new_avg)),bquote(Em.SD==.(new_std)), bquote(Th.Mean ==.(theor_avg)), bquote(Th.SD==.(theor_sd))) leg

[R] Renaming names in R matrix

I have the following matrix: > dat [,1] [,2] [,3][,4] foo 0.7574657 0.2104075 0.02922241 0.002705617 foo 0.000 0.000 0. 0.0 foo 0.000 0.000 0. 0.0 foo 0.000 0.000 0. 0.0 foo 0.000 0

[R] Alternative to heat.color(x)

The colors generated by heat.color(x) is too saturated. Where is there alternative command similar to that but "non-heated' which also I can input the value 'x'. - G.V. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

[R] How to plot diagonal line at any coordinate range in R

Dear expert How can we plot diagonal across (from bottom-left-hand corner to top right-hand corner), at any given coordinate range For example > plot(c(-2,3), c(-1,5), type = "n", xlab="x", ylab="y", asp = 1) or > plot(c(0,1000), c(0,334), type = "n", xlab="x", ylab="y", asp = 1) I tried abline

[R] Howto plot ROC Curve Directly from SN/PPV

Dear expert, Given such data: #Cutpoint SN (1-PPV) 5 0.560.01 7 0.780.19 9 0.910.58 How can I plot ROC curve with R that produce similar result like the attached file? I know ROCR package but it doesn't take such input. - GV _

Re: [R] How to Plot Two Curves Into One Page

, main=""); > plot(bar,lwd=2,lty=3,col="blue"); > legend(0.6,0.6,c('Default','Probabilistic'), col=c('red','blue'),lwd=3); > > A second option would be setting up a suitable layout. For this, please take > a look at ?layout. > B

[R] How to Plot Two Curves Into One Page

I have a R script that contain these lines for plotting: plot(foo,lwd=2,lty=3,col="red", main=""); plot(bar,lwd=2,lty=3,col="blue"); legend(0.6,0.6,c('Default','Probabilistic'), col=c('red','blue'),lwd=3); But it generate 1 file (Rplot.pdf) with two pages. Each page for 1 plot. Is there a way I

[R] List of List in Data Frame

Dear sirs, I have a data that is generated like this: > dat1 <- data.frame(V1 = rep(1, 5), V2 = sample(c(40:45), 5)) > dat2 <- data.frame(V1 = sample(c(0,1), 5, replace = TRUE), V2 = > sample(c(40:45), 5, replace = TRUE)) What I want to do is to obtain a data frame that contain list of list. >

Re: [R] How to Create Nested Data Frame

1 43 4 1 43 5 1 24 6 0 24 - G.V. > > Ivan > > > Le 1/31/2011 10:50, Gundala Viswanath a écrit : >> >> Dear Experts, >> >> I have a data that looks like this. >> >>> file1="dat1.tab" >&

[R] How to Create Nested Data Frame

Dear Experts, I have a data that looks like this. > file1="dat1.tab" > file2="dat2.tab" > dat1<-read.table(file1) > print(dat1) V1 V2 1 1 43 2 1 43 3 1 43 > > dat2<-read.table(file2) > print(dat2) V1 V2 1 1 43 2 1 21 3 1 43 4 1 43 5 1 24 6 0 24 > The column V1 refer to labels and V2

[R] Random Integer Number in Uniform Distribution

Is there a way to do it? At best what I can achieve is non integer: > runif(10, min=1, max=100) [1] 51.959151 56.654146 63.630251 3.172794 4.073018 11.977437 86.601869 [8] 75.788618 11.734361 6.770962 -G.V. __ R-help@r-project.org mailing list ht

[R] How To Extract Row from A Data Frame

I have a data frame that looks like this: > print(df) V2 V3 V4 V5 V6 V7 V8 V9V10V11V12 1 FN 8.637 28.890 31.430 31.052 29.878 33.215 32.728 32.187 29.305 31.462 2 FP 19.936 30.284 33.001 35.100 30.238 34.452 35.849 34.185 31.242 35.635 3 TN 0.000 17.190

[R] Accessing Element of a Table

I have the following structure: > str(propn) table [1:2(1d)] 0.674 0.326 - attr(*, "dimnames")=List of 1 ..$ label: chr [1:2] "o" "x" > print(propn) label o x 0.6738347 0.3261653 How can I access the value of "o" and "x" I tried this but fail > print(propn$label[,"o"]; -

[R] Accessing Vector of A Data Frame

I have a variable that looks like this: > print(pred$posterior) ox 1 2.356964e-03 9.976430e-01 2 8.988153e-01 1.011847e-01 3 9.466137e-01 5.338627e-02 4 2.731429e-11 1.00e+00 Now what I want to do is to access "o" and "x" How come this approach fa

[R] How to get a proportion of a Vector Member

I have a vector that looks like this: > foo [1] "o" "o" "o" "x" "o" "o" "o" "o" "o" "x" "x" "o" "x How can we find the percentage of "o" and "x" in that vector in R? - G.V __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-he

[R] What's the meaning of "Species ~ ." in IRIS data

I am refering to a function call like this: >data(iris) >x <- svmlight(Species ~ ., data = iris) I tried to see the content of it by typing: > Species ~ . but it gives nothing. How can I see it's content ? - P.Dubois __ R-help@r-project.org mailing

[R] Normalizing Vector with Negative Numbers

Dear expert, I have a series of number that looks like this x <- c(-0.005282, 0.000314, 0.002851, -2.5059217162, -0.007545, -1.0317758496, 0.001598, -1.2981735068, 0.072411) How can I normalize it in R so that the new numbers is ranging from 0 to 1 ? - G.V. ___

[R] Conditional Splitting a Vectors into Two Vectors

Suppose I have two vectors of same dimensions: x <-c(0.49534,0.80796,0.93970,0.8) count <-c(0,33,0,4) How can I group the vectors 'x' into two vectors: 1. Vector `grzero` that contain value in x with `count` value greater than 0 and 2. Vector `eqzero` with value in x with `cou

[R] How to Plot With Different Marker ( ‘x ’ and ‘o’) Based on Condition in R

Dear Expert, I have a data that looks like this: for_y_axis <-c(0.49534,0.80796,0.93970,0.8) for_x_axis <-c(1,2,3,4) count <-c(0,33,0,4) What I want to do is to plot the graph using "for_x_axis" and "for_y_axis" but will mark each point with "o" if the value is equal to 0(zero) and with

[R] Creating DataFrame of Vectors Data Structure for Classification

Dear Experts, I have a input file that looks like this -0.438185,svm,1 -0.766791,svm,1 0.695282,svm,-1 0.759100,svm,-1 0.034400,svm,1 0.524807,svm,1 -0.27647800,nn,1 -0.16120810,nn,-1 0.63911350,nn,1 0.400554110,nn,1 0.429192240,nn,-1 0.454239140,nn,1 How can I create a data structure in R so th

[R] Decreasing Cumsum Function?

Hi all, I have a frequency data that looks like this. 3 2 1 5 What I want to get is the "decreasing" cumulative of this data yielding 11 8 6 5 0 Is there any? I am aware of cumsum(), which will yield 3 5 6 11. But it is not what I want. - G.V. __

[R] How to plot two cumulative frequency graph together

Dear masters, I have data that looks like this: #val Freq1 Freq2 0.000 178 202 0.001 4611 5300 0.002 99 112 0.003 26 30 0.004 17 20 0.005 15 20 0.006 11 14 0.007 11 13 0.008 13 13 ...many more lines.. Full data can be found here: http://dpaste.com/173536/plain/ What I intend to do is to have a

[R] Filling Empty Column with String in read.table

I have a data file that looks like this. __DATA__ D7KAR5Z02F447V 176 G 0.22 D7KAR5Z02J3WLG 94 A 1.0529 D7KAR5Z02F4K6L 198 a 0.13 D7KAR5Z02J4SYO 67 C 0.9528 D7KAR5Z02J4SYO 83 C 1.0129 D7KAR5Z02J4SYO 97 T 0.13 D7KAR5Z02J4SYO 166 A 0.9427 I want the rows whe

[R] Fastest Way to Divide Elements of Row With Its RowSum

I have a data frame (dat). What I want to do is for each row, divide each row with the sum of its row. The number of row can be large > 1million. Is there a faster way than doing it this way? datnorm; for (rw in 1:length(dat)) { tmp <- dat[rw,]/sum(dat[rw,]) datnorm <- rbind(datnorm, tmp

[R] Truncating (not rounding) scientific value in R

How can I truncate the scientific value keeping two digits decimal. For example from: 6.95428812397439e-35 into 6.95e-35 -E.W. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://w

[R] Function to Normalize Numerical Vector in R

Is there any? - G.V. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

[R] How Does One Use the Value of Density Function?

How do people usually use the result of density function (e.g. dnorm)? Especially when its value can be greater than 1. What do they do with such density >1? > dnorm(2.02,2,.24) [1] 1.656498 - G.V. __ R-help@r-project.org mailing list https://stat.et

[R] Best Way to Compute/Approximate(?) Probabilty of a Point in a Given Distribution

AFAIK, R only has "pnorm" which computes the probability of getting a value smaller or equal to "x" from a normal distribution N[mean,stdev]. For example: R> pnorm(0, 4, 10) [1] 0.3446 means there is 34.46% chance of getting a value equal to or smaller than 0 from a N(4, 10) distribution. What

[R] Subsetting Data Frame based On Specified K Value

I have a data that looks like this: http://dpaste.com/88988/plain/ How can I extract/subset the data frame based on selected uniq ID. Let's say I want the first K uniq ID. I want to be able to specify the parameter "K" here, (i.e. given K=3, we hope to extract dat$V2 = 0,1,2). I'm stuck with thi

[R] Howto fit normal curve into histogram using GGPLOT2

Currently, I am doing it this way. x <- mtcars$mpg h<-hist(x, breaks=10, col="red", xlab="Miles Per Gallon", main="Histogram with Normal Curve") xfit<-seq(min(x),max(x),length=40) yfit<-dnorm(xfit,mean=mean(x),sd=sd(x)) yfit <- yfit*diff(h$mids[1:2])*length(x) lines(xfit, yfit, col="blue", lwd=

Re: [R] Howto Superimpose Multiple Density Curves Into One Plot

of. > ~ Sir Ronald Aylmer Fisher > > The plural of anecdote is not data. > ~ Roger Brinner > > The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > -

Re: [R] Howto Superimpose Multiple Density Curves Into One Plot

t; The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > -Oorspronkelijk bericht- > Van: Gundala Viswanath [mailto:gunda...@gmail.com] > Verzonden: woensdag 2 se

Re: [R] Howto Superimpose Multiple Density Curves Into One Plot

> The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > -Oorspronkelijk bericht- > Van: Gundala Viswanath [mailto:gunda...@gmail.com] > Verzonden: woensd

Re: [R] Howto Superimpose Multiple Density Curves Into One Plot

ble to say what > the experiment died of. > ~ Sir Ronald Aylmer Fisher > > The plural of anecdote is not data. > ~ Roger Brinner > > The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body

Re: [R] Howto Superimpose Multiple Density Curves Into One Plot

for an answer does not > ensure that a reasonable answer can be extracted from a given body of > data. > ~ John Tukey > > -Oorspronkelijk bericht- > Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > Namens Gundala Viswanath > Verzonden: woensd

[R] Howto Superimpose Multiple Density Curves Into One Plot

I have a data that looks like this: http://dpaste.com/88561/plain/ And I intend to create multiple density curve into one plot, where each curve correspond to the unique ID. I tried to use "sm" package, with this code, but without success. __BEGIN__ library(sm) dat <- read.table("mydat.txt"); pl

[R] Normalized Y-axis for Histogram Density Plot

I have the following data which I tried to draw the probability density plot. Here is the code I have: x <- read.table("mydat.txt"); d <- rep(x$V2,times=x$V3); hist(d,probability=T, xlab="FlowSignal"); But why the y-axis range from 0 to 6, instead of 0 to 1? What's the correct way to plot it?

[R] How to extract integer in a data frame

ata frame where the entry in V1 has (x.000) as its decimal. yielding > wanted_dat V1 V2 V3 1 0.000 2 554889 2 123.000 03209 What's the way to do it in R? - Gundala Viswanath Jakarta - Indonesia _

[R] Coloring X, Y and Main Label

Dear all, I have no problem coloring the axis and plot, following these procedures: http://www.nabble.com/Coloring-X-and-Y-axis-tt22989739r0.html#a22989739 However the X,Y and Main Label stays in black. How can we change their colors? - Gundala Viswanath Jakarta - Indonesia

[R] How to control distance between rows of figures in multiple plots

Dear all, I have a plot with 2 x 2 figures matrix in it. pdf("~/Desktop/myplot.pdf",width=13,height=7) par(mfrow=c(2,2)) # follow by some code Now the distance between figures of row 1 and row 2 is too wide. How can I modify? - Gundala Viswanath Jakarta -

[R] Coloring X and Y axis

Dear all, Is there a way to do it? The following code: > pdf("test.pdf") > plot(1,1,col="red") > dev.off() Only colors the plot into red, but not x and y axis (inclusive the tick marks). - Gundala Viswanath Jakarta - Indonesia __

[R] Howto Plot With Transparent Background

Is there a way to do it in R? Especially generating plot in EPS/PDF format. By transparent I mean clear (not white) background. I want to attached it to dark PPT slides. - Gundala Viswanath __ R-help@r-project.org mailing list https://stat.ethz.ch

[R] Filling in Gapped Interval of a Data Frame As Series

33.2 16 6 44.5 17 7 5.00 Is there a way to do it in R? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/p

[R] How to force an point in x-axis to appear in plot

marks. - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained

[R] Howto Disable Scientific Numeric in X-axis for Plotting

- Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible

[R] Barplot With Selected X-Axis Region

27;s wrong with my approach. So yes, I do want the V1 information, hence I am aware that I dont' want: > plot(hist(dat[dat >=-500 & dat <=500])) - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://sta

[R] Howto Supress Extra Blank Page in gridBase

__ library(grid) library(gridBase) opar <- par(no.readonly=TRUE) par(opar) grid.newpage() pushViewport(viewport(width=0.5, height=0.5)) grid.rect(gp=gpar(col="grey", lty="dashed")) par(omi=gridOMI()) par(mfrow=c(2, 2), mfg=c(1, 1), mar=c(3, 3, 1, 0)) for (i in 1:4) { plot(1:10

[R] Simple Plot with Grid's Viewport

;, j, "\n", sep="") test.plot(i,j); } } dev.off() __END__ - Gundala Viswanath __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/post

[R] Cumulative Plot with Given X-Axis

0.015241 6 0.0141398 0.0142373 7 0.0101515 0.0102948 8 0.0308843 0.031294 9 0.0095504 0.00960626 10 0.00729676 0.0073713 - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mai

[R] Invalid Type of Char Argument When Sum() is Used

7;s wrong with the data type so that it gives such error? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-g

[R] Modifying Names from (x,y] into x

Hi, I have the following data that looks like this: > names(dat) [1] "(-2329,-2319]" "(-1399,-1389]" "(-669.4,-659.4]" How can I modify those names into just this? [1] -2329 -1399 -669.4 - Gund

[R] Insert value in a Vector Alternately

V11V12 V13V14 V15 V16 0 0.00380959 0.00380959 0.00380959 0 .00380083 0.00380083 0.00380083 Is there a quick way to do it in R? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list ht

Re: [R] Barplot with Sorted X-Axis

Hi Jim, > or sorting the columns of the above table if that is what you are using to > plot. How do you do that? Yes I am using that data exactly for the plotting. - GV. > > Jim > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/

[R] Barplot with Sorted X-Axis

the second bar (value = 76) id placed on the right to the first. (8.048,18.05] (-21.95,-11.95] 81 76 This is the command I use to plot: barplot(x,ylab="Number of Unique Tags", xlab="Expected - Observed") - Gundala Viswanath

[R] Remove top-K elements in Vector

Hi all, Suppose I hve this vector: > x [1] 3 4 7 17 22 12 15 12 3 3 1 1 How can I remove the top-3 element. Yielding only: [1] 17 22 12 15 12 3 3 1 1 - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list ht

[R] Plotting Binned Data

RL http://docs.google.com/Doc?id=dcvdrfrh_5cm5qkchw How can I fix the code so that it gives a exact plot to "dat" above, with same number of bins and its respective frequency? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list h

Re: [R] Generating Numbers With Certain Distribution in R

Dear all, Thanks so much, the latest version by Gustav work just fine. In the first version, the outcome is more digital than contiguous. - Gundala Viswanath Jakarta - Indonesia On Wed, Feb 11, 2009 at 10:35 PM, Gustaf Rydevik wrote: > On Wed, Feb 11, 2009 at 2:15 PM, Ben Bolker wr

[R] Generating Numbers With Certain Distribution in R

Dear all, Is there a way to generate K numbers of integer (K = 10^6). The maximum value of the integer is 200,000 and minimum is 1. And the occurrences of this integer follows a lognormal distribution. - Gundala Viswanath Jakarta - Indonesia __ R

[R] Meaning of Inner Product (%*%) Between Slot and Vector

0.200 [4,] 0.200 [5,] 0.200 My questions are: 1. How does %*% work in the above example? 2. Is there a more understandable (naive) way to implement such product in this context? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.or

Re: [R] Faster Printing Alternatives to 'cat'

es = TRUE, qmethod = c("escape", "double")) - Gundala Viswanath Jakarta - Indonesia On Sun, Jan 18, 2009 at 12:09 AM, Henrik Bengtsson wrote: > Do it in chunks of rows. /H > > On Sat, Jan 17, 2009 at 6:55 AM, Gundala Viswanath wrote: >> Hi Hadley, >> >

Re: [R] Faster Printing Alternatives to 'cat'

tried your suggestion already, I have memory problem > x <- cbind(dat$V1, as.character(dat$V2)) Error: cannot allocate vector of size 4.2 Gb Execution halted - Gundala Viswanath Jakarta - Indonesia On Sat, Jan 17, 2009 at 11:39 PM, hadley wickham wrote: > On Sat, Jan 17, 2009 at 7:59

Re: [R] Value Lookup from File without Slurping

Hi, > Unless you specify an in-memory database the database is stored on disk. Thanks for your explanation. I just downloaded 'sqldf'. Where can I find the option for that? In sqldf I can't see the command. I looked at: envir = parent.frame() doesn't appear to be the on

Re: [R] Value Lookup from File without Slurping

ssue? Why is that? Sorry for my naive question. - Gundala Viswanath Jakarta - Indonesia On Fri, Jan 16, 2009 at 9:09 PM, Gabor Grothendieck wrote: > On Fri, Jan 16, 2009 at 5:52 AM, r...@quantide.com wrote: >> I agree on the database solution. >> Database are the rigth too

[R] Value Lookup from File without Slurping

ding value for each query above, yielding: 0.02 0.7 However, I want to avoid slurping whole repo.txt into an object (e.g. hash). Is there any ways to do that? The reason I want to do that because repo.txt is very2 large size (milions of lines, with tag length > 30 bp), and my PC memory i

Re: [R] Summary of Total Object.Size in R Script

Sorry for my late reply. Thank you so much Jim. This script of yours is very2 useful. I have used it. - Gundala Viswanath Jakarta - Indonesia On Wed, Jan 14, 2009 at 12:17 AM, jim holtman wrote: > Here is a function I use to see how big the objects in my workspace are: > &g

[R] Obtain numbers from vector of NAs and numbers

ain all. [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 9 18 8 17 18 [26] 13 9 5 6 7 9 10 11 13 14 3 17 2 1 14 3 3 13 4 4 16 Is there a quick way to do it? I tried "grep("[0-9]", vect)" but fail. - Gundala Viswan

[R] Howto access object of object

22 22 22 22 Slot "dimension": [1] 100 1 __ END__ How can I acces "Slot 'ra'" only? I tried print(x$ra) but fail. - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz

[R] Summary of Total Object.Size in R Script

oesn't give the exact byte size. - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide comm

Re: [R] Extracting Hash via Vector

Thanks for your most reasonable reply, Henrique. - Gundala Viswanath Jakarta - Indonesia On Tue, Jan 13, 2009 at 8:01 PM, Henrique Dallazuanna wrote: > Try this: > > unlist(ifelse(q %in% names(x), x[q], NA)) > > On Tue, Jan 13, 2009 at 8:49 AM, Gundala Viswanath > wro

[R] Extracting Hash via Vector

But why this failed? > extracted <- x[[q]] Error in x[[q]] : subscript out of bounds we expect the output of 'extracted' to be a vector as well. When the key is not present to give "NA" in vector - Gundala Viswanath Jakarta - Indonesia ___

Re: [R] Converting Factor to Vector

t; "AAC" "AAG" "ATA" "ATT"... > >> print(new_repo) > [1] "AAA" "AAT" "AAC" "AAG" "ATA" "ATT"... - Gundala Viswanath Jakarta - Indonesia On Tue, Jan 13, 2009 at 2:40 PM, wrote:

[R] Converting Factor to Vector

hr [1:100] "AAA" "AAT" "AAC" "AAG" "ATA" "ATT"... > print(new_repo) [1] "AAA" "AAT" "AAC" "AAG" "ATA" "ATT"... I tried as.vector(), but it remains the same factor. - Gundala V

Re: [R] Fast way to finding index in Vector

"ABDCA" "ACACC" "DADAA" > "ABCAD" ... >> str(z) > chr [1:200] "EAEDC" "DACCD" "BEAAD" "CDDDA" "ABDCA" "ACACC" > "DADAA" "ABCAD" ... >> system.time(y <- matc

Re: [R] Fast way to finding index in Vector

Yes Jim, exactly. BTW, I found from ?match " Matching for lists is potentially very slow and best avoided except in simple cases." Since I am doing this for million of tags. Is there a faster alternatives? - Gundala Viswanath Jakarta - Indonesia On Tue, Jan 13, 2009 at 12:

[R] Returning Non-Unique Index with Which (alternatives?)

hat the query contain repeating elements, yet the output of which only returns unique. How can I make it returning [1] 3 6 6 instead? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/

Re: [R] Fast way to finding index in Vector

Hi Jorge and all, How can I modified your code when query size can be bigger than repository, meaning that it can contain repeats. e.g. qr <- c("AAC", "ATT", "ATT","AAC", "ATT", "ATT", "AAT", "ATT", &qu

[R] Fast way to finding index in Vector

index in repository in a fast way. Giving: [1] 3 6 Typically the size of repo is around ~12million element, and query around ~1 million element. - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.

[R] Can't Destroy Dim Names

AAAT" ... I want to destroy the attribute yielding only this: > str(mat) Named chr [1:32268] "yQAAA" "jQAAQ" "UQAAg" "FQAAw" "1QABA" ... But why this command fail to do it? > dimnames(mat) <- NULL Btw, the object size for

[R] Converting Numerical Matrix to List of Strings

of Column in matrix = length of string (= 3) 2. Number of Row in matrix = length of vector ( = 4). 3. Character "a" encode as "0", "c" -> "1", "g" -> "2", "t" -> "3" Length of strings are

[R] Pack and Unpack Strings in R

'b*', $string; print "COMP: $compressed\n"; printf "%d bytes\n", length $compressed; my @data; # Store the compressed bit into array push @data, $compressed; # process the array foreach my $dat ( @data ) { my $decompressed = unpack 'b*', $dat; $decompressed

[R] Extracting File Basename without Extension

Dear all, The basename() function returns the extension also: > myfile <- "path1/path2/myoutput.txt" > basename(myfile) [1] "myoutput.txt" Is there any other function where it just returns plain base: "myoutput" i.e. without 't

Re: [R] Faster Printing Alternatives to 'cat'

favorite questions; "tell me what you > want to do, not how you want to do it". > > On Thu, Jan 8, 2009 at 6:12 AM, Gundala Viswanath wrote: >> Dear all, >> >> I found that printing with 'cat' is very slow. >> >> For example in my mach

[R] Faster Printing Alternatives to 'cat'

s already very large (>2Gb) for ( s in 1:length(x) ) { cat(as.character(foo[s]),"\t",bar[s],"\t", qux[s],"\n") } __END__ for "x" of size ~1.5million, takes more than 10 hours to print. On my Linux 1994.MHz AMD processor. Is there any faster al

[R] Function to Check Object's Memory Size

Dear all, Does R has any function that measures how much memory hold by any particular object? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] Destroying Attributes of a Matrix

0 0 0 0 0 0 0 0 ... - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contain

[R] Changing Matrix Header

0 0 0 0 0 0 [2,] 0 0 0 0 0 0 0 0 0 1 [3,] 0 0 0 0 0 0 0 0 02 I tried: > as.matrix(x) But failed. - Gundala Viswanath Jakarta - Indonesia __

[R] Encoding Vector of Strings into Numerical Matrix

3 0 In principle: 1. Number of Column in matrix = length of string (= 3) 2. Number of Row in matrix = length of vector ( =4). 3. Character "a" encode as "0", "c" -> "1", "g" -> "2", "t" -> "3"

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