Re: [R] Writing a summary file in R
gt;=1)/nrow(x) )) ) ) > # You often need the t() function when working with apply functions > > df > chr strt end frac > chr1 100 chr1 100 1591 > chr1 200 chr1 200 2601 > chr1 500 chr1 500 7501 > chr11 679 chr11 679 687 0.5 > chr22 100 chr22 100 2001 > chr22 300 chr22 300 4000 > chr3 450 chr3 450 7001 > chr4 100 chr4 100 300 0.5 > chr7 350 chr7 350 600 0.5 > chr9 100 chr9 100 1251 > > > as.data.frame(t(sapply(splinp, function(x) summary(x > $methylation )) ) ) >Min. 1st Qu. Median Mean 3rd Qu. Max. > chr1 100 0.04 0.0425 0.045 0.045 0.0475 0.05 > chr1 200 0.12 0.1200 0.120 0.120 0.1200 0.12 > chr1 500 0.09 0.0900 0.090 0.090 0.0900 0.09 > chr11 679 0.00 0.0175 0.035 0.035 0.0525 0.07 > chr22 100 0.03 0.0425 0.055 0.055 0.0675 0.08 > chr22 300 0.00 0. 0.000 0.000 0. 0.00 > chr3 450 0.03 0.0300 0.030 0.030 0.0300 0.03 > chr4 100 0.00 0.0125 0.025 0.025 0.0375 0.05 > chr7 350 0.00 0.0150 0.030 0.030 0.0450 0.06 > chr9 100 0.10 0.1000 0.100 0.100 0.1000 0.10 > > # The coup de grace: bind the columns together > > > df.summ <- as.data.frame(t(sapply(splinp, function(x) summary(x > $methylation )) ) ) > > cbind(df, df.summ) > chr strt end frac Min. 1st Qu. Median Mean 3rd Qu. Max. > chr1 100 chr1 100 1591 0.04 0.0425 0.045 0.045 0.0475 0.05 > chr1 200 chr1 200 2601 0.12 0.1200 0.120 0.120 0.1200 0.12 > chr1 500 chr1 500 7501 0.09 0.0900 0.090 0.090 0.0900 0.09 > chr11 679 chr11 679 687 0.5 0.00 0.0175 0.035 0.035 0.0525 0.07 > chr22 100 chr22 100 2001 0.03 0.0425 0.055 0.055 0.0675 0.08 > chr22 300 chr22 300 4000 0.00 0. 0.000 0.000 0. 0.00 > chr3 450 chr3 450 7001 0.03 0.0300 0.030 0.030 0.0300 0.03 > chr4 100 chr4 100 300 0.5 0.00 0.0125 0.025 0.025 0.0375 0.05 > chr7 350 chr7 350 600 0.5 0.00 0.0150 0.030 0.030 0.0450 0.06 > chr9 100 chr9 100 1251 0.10 0.1000 0.100 0.100 0.1000 0.10 > > -- > Best; > > David. > >> >> On Wed, Jul 27, 2011 at 4:02 PM, a217 <aj...@case.edu> wrote: >>> Hello, >>> >>> I have an input file: >>> http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt >>> >>> where col 1 is chromosome, column2 is start of region, column 3 is >>> end of >>> region, column 4 and 5 is base position, column 6 is total reads, >>> column 7 >>> is methylation data, and column 8 is the strand. >>> >>> >>> I would like a summary output file such as: >>> http://r.789695.n4.nabble.com/file/n3700031/out.summary.txt >>> out.summary.txt >>> >>> where column 1 is chromosome, column 2 is start of region, column 3 >>> is end >>> of region, column 4 is total reads in general, column 5 is total >>> reads >=1, >>> column 6 is (col4/col5) or the percentage, and at the end I'd like >>> to list 6 >>> more columns based on summary results from summary() function in R. >>> >>> The summary() function will be used to analyze all of the >>> methylation data >>> (col7 from input) for each region (bounded by col2 and col3). >>> >>> For example for chr1 100 159 summary() gives: >>> Min. 1st Qu. MedianMean 3rd Qu.Max. >>> 0.0400 0.0425 0.0450 0.0450 0.0475 0.0500 >>> >>> which is simply the methylation data input into summary() only in >>> the region >>> of chr1 100 159. >>> >>> I know how to perform all of the required functions line-by-line, >>> but the >>> hard part for me is essentially taking the input data with multiple >>> positions in each region and assigning all of the summary results >>> to one >>> line identified by the region. >>> >>> If any of you have any suggestions I would appreciate it. >>> >>> -- >>> View this message in context: >>> http://r.789695.n4.nabble.com/Writing-a-summary-file-in-R-tp3700031p3700031.html >>> Sent from the R help mailing list archive at Nabble.com. >>> >>> __ >>> 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-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. > > David Winsemius, MD > West Hartford, CT > > __ > 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. > -- View this message in context: http://r.789695.n4.nabble.com/Writing-a-summary-file-in-R-tp3700031p3716837.html Sent from the R help mailing list archive at Nabble.com. __ 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] Counting rows given conditional
Hello, I have an input file that contains multiple columns, but the column I'm concerned about looks like: "TR" 5 0 4 1 0 2 0 To count all of the rows in the column I know how to do NROW(x$TR) which gives 7. However, I would also like to count only the number of rows with values >=1 (i.e. not 0). I've tried NROW(x$TR>=1) which did not give the intended output. Do any of you have any suggestions as to where I'm going wrong? -- View this message in context: http://r.789695.n4.nabble.com/Counting-rows-given-conditional-tp3718541p3718541.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Loops for repetitive task
Hello,
I have an R script that I use as a template to perform a task for multiple
files (in this case, multiple chromosomes).
What I would like to do is to utilize a simple loop to parse through each
chromosome number so that I don't have to type the same code over and over
again in the R console.
I've tried using:
for(i in 1:22){
etc..
}
and replacing each chromosome number with [[i]], but that did not seem to
work.
Below is the script I have. Basically everywhere you see a '2' I would like
there to be an 'i' so that the script can be applied in a general sense.
Code###
chr2.data<-read.table(file="chr2.out.txt", header=F)
colnames(chr2.data)<-c("chr","start","end","base1","base2","totalreads","methylation","strand")
splc2<-split(chr2.data, paste(chr2.data$chr))
chr2.df<-as.data.frame(t(sapply(splc2, function(x)
list(TR=NROW(x[['totalreads']]),RG1=sum(x[['totalreads']]>=1),
percent=(NROW(x[['totalreads']]>=1)/sum(x[['totalreads']]))
chr2.df.summ<-as.data.frame(t(sapply(splc2, function(x)
summary(x$methylation
chr2.summ<-cbind(chr2.df,chr2.df.summ)
##
Here are some sample input files in case you'd like to test the code:
##
# chr1.out.txt
##
chr1100 159 104 104 1 0.05+
chr1100 159 145 145 1 0.04+
chr1200 260 205 205 1 0.12+
chr1500 750 600 600 1 0.09+
##
# chr2.out.txt
##
chr2100 200 105 105 1 0.03+
chr2100 200 110 110 1 0.08+
chr2300 400 350 350 0 0 +
The code works perfectly fine just typing everything out by hand, but that
is very inefficient given that there are 24 chromosomes for each dataset. I
am just looking for any suggestions as to how I can write a general version
of this code.
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[R] Generating a histogram with R
Hello, I have a sample file: chr22 100 150 125 21 0.145 + chr22 200 300 212 13 0.05+ chr22 345 365 351 12 0.09+ chr22 500 750 510 15 0.10+ chr22 500 750 642 9 0.02+ chr22 800 900 850 10 0.05+ where I need to generate a histogram from the data in column 6 (i.e. 0.145, 0.05, etc.). To make it easier to read, I would plot the data as 1-0.05=0.95 for all of the data in column 6. What I would like to know is how to generate a histogram with the data from one file? Also, would I be able to generate one histogram from multiple files as well (with the same format)? For example, I have multiple files in the same format as the sample file above, and I would like to make one histogram for all column six data in all files. Thank you, a217 -- View this message in context: http://r.789695.n4.nabble.com/Generating-a-histogram-with-R-tp3663350p3663350.html Sent from the R help mailing list archive at Nabble.com. __ 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] Writing a summary file in R
Hello, I have an input file: http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt where col 1 is chromosome, column2 is start of region, column 3 is end of region, column 4 and 5 is base position, column 6 is total reads, column 7 is methylation data, and column 8 is the strand. I would like a summary output file such as: http://r.789695.n4.nabble.com/file/n3700031/out.summary.txt out.summary.txt where column 1 is chromosome, column 2 is start of region, column 3 is end of region, column 4 is total reads in general, column 5 is total reads >=1, column 6 is (col4/col5) or the percentage, and at the end I'd like to list 6 more columns based on summary results from summary() function in R. The summary() function will be used to analyze all of the methylation data (col7 from input) for each region (bounded by col2 and col3). For example for chr1 100 159 summary() gives: Min. 1st Qu. MedianMean 3rd Qu.Max. 0.0400 0.0425 0.0450 0.0450 0.0475 0.0500 which is simply the methylation data input into summary() only in the region of chr1 100 159. I know how to perform all of the required functions line-by-line, but the hard part for me is essentially taking the input data with multiple positions in each region and assigning all of the summary results to one line identified by the region. If any of you have any suggestions I would appreciate it. -- View this message in context: http://r.789695.n4.nabble.com/Writing-a-summary-file-in-R-tp3700031p3700031.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] Writing a summary file in R
Yes, that is the general objective. I'll look-into aggregates in R and see if anything helps. Thanks, a217 -- View this message in context: http://r.789695.n4.nabble.com/Writing-a-summary-file-in-R-tp3700031p3700071.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] Writing a summary file in R
Thank you both very much! The codes are pretty slick and should greatly help me in my task. -- View this message in context: http://r.789695.n4.nabble.com/Writing-a-summary-file-in-R-tp3700031p3700382.html Sent from the R help mailing list archive at Nabble.com. __ 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] Histogram for each ID value
I have a dataframe in the general format: chr1 0.5 chr1 0 chr1 0.75 chr2 0 chr2 0 chr3 1 chr3 1 chr3 0.5 chr7 0.75 chr9 1 chr9 1 chr22 0.5 chr22 0.5 where the first column is the chromosome location and the second column is some value. What I'd like to do is have a histogram created for each chr location (i.e. a separate histogram for chr1, chr2, chr3, chr7, chr9, and chr22). I am just having a hard time getting everything to work out and am hoping for some suggestions. -- View this message in context: http://r.789695.n4.nabble.com/Histogram-for-each-ID-value-tp3911791p3911791.html Sent from the R help mailing list archive at Nabble.com. __ 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] replacing percentage of values in data frame
I've been looking for how to change a certain percentage of values in a data
frame, but I've been struggling to find information in R.
For example:
#example data##
> data
V1V2V3 V4 V5 V6 V7
1 chr1 500 500 CHH 0 0.5 +
2 chr1 550 550 CHH 0 0.0 +
3 chr2 700 700 CHH 0 0.0 +
4 chr2 1000 1000 CHH 0 0.0 +
5 chr3 100 100 CHH 0 0.0 +
6 chr4 450 450 CG 0 0.0 +
7 chr5 450 450 CHH 0 0.0 +
8 chr5 50034 50034 CHG 0 0.0 +
9 chr7 50055 50055 CHG 0 0.0 +
10 chr10 50063 50063 CHH 0 0.0 +
> dput(data)
structure(list(V1 = structure(c(1L, 1L, 3L, 3L, 4L, 5L, 6L, 6L,
7L, 2L), .Label = c("chr1", "chr10", "chr2", "chr3", "chr4",
"chr5", "chr7"), class = "factor"), V2 = c(500L, 550L, 700L,
1000L, 100L, 450L, 450L, 50034L, 50055L, 50063L), V3 = c(500L,
550L, 700L, 1000L, 100L, 450L, 450L, 50034L, 50055L, 50063L),
V4 = structure(c(3L, 3L, 3L, 3L, 3L, 1L, 3L, 2L, 2L, 3L), .Label =
c("CG",
"CHG", "CHH"), class = "factor"), V5 = c(0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L), V6 = c(0.5, 0, 0, 0, 0, 0, 0, 0,
0, 0), V7 = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L), .Label = "+", class = "factor")), .Names = c("V1", "V2",
"V3", "V4", "V5", "V6", "V7"), class = "data.frame", row.names = c(NA,
-10L))
>
Say for instance, I'd like to change 20% of values in column 6 to '1'
instead of zero or whatever value may be currently present. How would I
approach this?
I am working with a large data frame and I need to replace values in one of
the columns for 10-20% of the entire dataset. I hope what I am trying to
convey is understandable to you.
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[R] Help with increasing the speed of script
I actually have two questions regarding the same script:
#
data <- vector('list', 24)
splc <- vector('list',24)
df.summ <- vector('list',24)
for (i in 1:length(chrData))
{
data[[i]] <- read.table(file=paste('chr',i,'.nonCG.covered.out',sep=''),
header=F)
colnames(chrData[[i]])<-c("chr","start","end","tot","methy")
splc[[i]]<-split(data[[i]], paste(data[[i]]$chr, data[[i]]$start,
data[[i]]$end))
df.summ[[i]]<-as.data.frame(t(sapply(splc[[i]], function(x)
summary(1-x$methylation
cat("finished reading",paste('chr',i),date(),"\n")
}
#
1) I'll start off first with perhaps the easier question. The above script
is a portion of r code that I run from batch through a pipeline. I've
decided that any process that takes longer than 5 minutes to complete should
include some measure of progress so that the user doesn't just sit there and
wonder if the code is working or not.
So I've tried the command:
R CMD BATCH -q test.R /dev/tty
which gives the same output as .Rout file would. What I am hoping to
accomplish is to only print the "cat()" results from batch instead of the
entire script.
2) The second issue I have is with the speed of the script. Specifically,
the slow point of the script is:
splc[[i]]<-split(data[[i]], paste(data[[i]]$chr, data[[i]]$start,
data[[i]]$end))
It may operate in quadratic or exponential time (I haven't specifically run
tests) because as the input data increases in size, the time the script
takes longer than a constant-time script would run.
Perhaps the more experienced programmers among you could give me a few
hints/suggestions so that I can head in the right direction.
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