.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: Peter Alspach [peter.alsp...@plantandfood.co.nz]
Sent: 31 October 2011 22:08
To: Bansal, Vikas; r-help@r-project.org
Subject: RE: Plot two matrices and keeping the record of
is coming fine.But I am loosing the row names,therefore I have no idea
which patients are on the top right corner of the plot.
Can you please help me.I will be very thankful to you.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
[[alternative HTML
which patients are on the top right corner of the plot.
Can you please help me.I will be very thankful to you.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
[[alternative HTML version deleted]]
__
R-help@r
i.out),fill=T,colClasses = "character")
then it is not working.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: istaz...@gmail.com [istaz...@gmail.com] On Behalf Of Ista Zahn
[iz...@psych.rochester.edu]
Sent: Mo
if you will check this line-
df=read.table($i.out,fill=T,colClasses = "character")
I have used $i.out here and every time in for loop i will be 1 then 2 then 3
till 100.So it will become very easy.But this $ sign is not working in the
R.Can I do this thing in R.
$f.".out";
I have tried this thing in R but it does not work.Can somebody please help me.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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values.My data frame has lot of
rows(approx. ).
Can you please help me with this.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: R. Michael Weylandt [michael.weyla...@gmail.com]
Sent: Wednesday, August 17, 2011
returning the index for two largest value with-
sort.int(df,index.return=TRUE)$ix[c(4,3)]
but it does not accept data frame.
Can you please give some idea how to do this,because it is very tricky and
after studying a lot, I am not able to perform.Please help.
Thanking you,
Warm Regards
Vikas
please give some idea how to do this,because it is very tricky and
after studying a lot, I am not able to perform.Please help.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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https
1|2|3|4|5|6|7|8|10|~|H", "",x[5]))
this use of gsub looks odd to me,although result is coming good but I want
something fast because data is large.I want something like this-
delete everything else except A,a,C,c,G,g,T,t and dot and comma.
Any suggestions Please.
Thanki
Dear all,
Thanks to everyone.I tried both the methods and it is working.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: David Winsemius [dwinsem...@comcast.net]
Sent: Sunday, August 07, 2011 8:31 PM
To: peter
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide comm
..so on and 50th column is
51st..?I will be very thankful to you.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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PLEASE do read the posting
output of new data frame-
newdf
V1 V2 V3 V4 V5 V6 V7 V8V9V10
10 135349878 a A 11 0 0 7 ,..aaab^ab
10 135349912 g G 18 0 0 8 ,.., `_abXbba
Can you please help me.I will be very thankful to you.
Thanking you,
Warm Regards
Vikas Bansal
Msc
part; should be 'is.na':
so you would do:
repeat{
value <- as.numeric(readline())
if (!is.na(value)) break
}
On Mon, Jul 25, 2011 at 8:05 AM, Bansal, Vikas wrote:
> Thanks for your reply.But I have never seen ia.na in R.Can you please tell me
> how to use this?
Thanks for your reply.But I have never seen ia.na in R.Can you please tell me
how to use this?
So you are saying rather than is.numeric,I have to test user input by ia.na?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
ber Please enter numerical value
That is why I am confused now-I have tried with- value=as.numeric(value)
and without this also.But did not find any solution.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: Smart Guy [s
you please tell me what mistake I am doing?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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PLEASE do read the posting guide http://ww
Dear Jeff,
Thanks a lot for your reply.
I was just curious about this thing about grep that it can perform this kind of
thing or not. Otherwise with numerical comparison I know it is very easy to
do.Like-
df <- df[df$V5 >= 10, ]
Thanks a lot for your help.
Thanking you,
Warm Regards
13
5973 T 13 0 13
like in 5th column.If I want only rows whose value is more than 10 in 5th
column?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: Phil Spector [spec...@stat.berkeley.edu]
Sent: Monday, July 25
0 6 ,,,.,,
10 135349475 a A 8 0 0 6 ,,,.,,
10 135349477 a A 7 0 0 6 ,,,.,,
10 135349478 a A 11 0 0 6 ,,,.,,
Thanking you,
Warm Regards
Vi
not
stop even if user writes wrong name of input file?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: Bert Gunter [gunter.ber...@gene.com]
Sent: Sunday, July 24, 2011 3:58 PM
To: Bansal, Vikas
Cc: r-help@r-project.o
r the name of your file: ")
}
df=read.table(define(),fill=T,sep="\t",colClasses = "character")
##starline
if(## some condition here)
{
print("wrong name of the file Please enter again ")
## some goto function so that it should
internet but
did not find anything related to this.I will be very thankful to you.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: Joshua Wiley [jwiley.ps...@gmail.com]
Sent: Friday, July 22, 2011 9:48 PM
To: Bansal
?
lapply(c("file1", "file2", etc.), yourfunction)
From: Joshua Wiley [jwiley.ps...@gmail.com]
Sent: Friday, July 22, 2011 8:26 PM
To: Bansal, Vikas
Cc: r-help@r-project.org
Subject: Re: [R] User input(unknown name and number of files)
On Fri, J
df,row.names=F), file = "end.txt", append =
FALSE)
I know it should do it with for loop and an array.I want that if user input 12
files,the dataframe name df should be different for all the 12 files.
Can you please tell me how can I do this.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioin
hould do it with for loop and an array.I want that if user input 12
files,the dataframe name df should be different for all the 12 files.
Can you please tell me how can I do this.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
__
hould do it with for loop and an array.I want that if user input 12
files,the dataframe name df should be different for all the 12 files.
Can you please tell me how can I do this.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
__
= file['Pos'], FUN = sum)
Error in FUN(X[[1L]], ...) : invalid 'type' (character) of argument
the thing is I cant use the plyr because I want the coding so that I can use it
to make a tool.
Can you please tell me why aggregate function is showing this error.I am
confuse
= df['Pos'], FUN = sum)
Error in aggregate.data.frame(file[vars], by = df["Pos"], FUN = sum) :
arguments must have same length
the thing is I cant use the plyr because I want the coding so that I can use it
to make a tool.
Can you please tell me why aggregat
0.00 48.00 0.0024.00
10 135344126 0.00 0.0024.00 0.00
Can you please help me.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College LondonDear all,
I have one problem and did not find any solution.
I have a file(file.txt) attac
I have tried that also.But it is showing this error-
aggregate(file[,3:6], by = list(file[,2]), FUN = sum)
Error in FUN(X[[1L]], ...) : invalid 'type' (character) of argument
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings Coll
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: Bansal, Vikas
Sent: Thursday, July 14, 2011 6:07 PM
To: Bert Gunter
Subject: RE: [R] Adding rows based on column value
Yes sir.I am trying.
I am using this-
aggregate
I have checked it but did not get any results.Is there a way I can do it?I will
be very thankful to you.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: Bert Gunter [gunter.ber...@gene.com]
Sent: Thursday, July 14
48.00 0.0024.00
10 135344126 0.00 0.0024.00 0.00
Can you please help me.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London Chr Pos CaseA CaseC CaseG CaseT
10 135344110 0.00 24.00 0.0
to enter the value of ind from user.Can you please tell me how can i
remove this error.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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12
because sum of 3rd,4th,5th and 6th column is 1 for first row.and for case A,C
and T if we will apply above formula the answer will be zero (0/1)*12*2 which
is equal to 0 but for Case G-
(1/1)*12*2 which is equal to 24.
Can you please help me.
Thanking you,
Warm Regards
Vikas B
i did not know how to do it.
Can you please help me.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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PLEASE do read the posting guide ht
I used this code by Jim Holtman (Thanks to him)and it is working perfectly.
dfa$value <- sapply(dfa$V10, function(a) paste(as.integer(charToRaw(a)),
collapse = ' '))
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
91 94
31 0 2 T 89 94
32 0 2 GG96 93
so in output 15th and 27th row should be deleted and 31st row should be-
31 0 2 T89 94
because 89 is score for A and 94 is score for T.Therefore A has been deleted
because its score is less than 90.
Can you help me please.
5 0 1 CX
16 0 1 C`
17 0 1 Ga
18 0 1 G_
Column V10 contains ASCII values.I want to convert them into decimal.
Can you please help me.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London V7 V8 V9 V10
0 1 G`
0 1 Ta
=lapply(df[,4], function(c) as.numeric(charToRaw(c)))
I want to ask that,is this the right way to convert these values into decimal?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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https
So i think I am doing mistake in converting ASCII values in col V10 in my data
frame (dfa.).can you please tell me that, is this the right way to convert
ASCII values into decimal-
dfa$V10=lapply(dfa[,4], function(c) as.numeric(charToRaw(c)))
Thanking you,
Warm Regards
Vikas Bansal
Msc
97
First row should be deleted because it contains 82 which is less than 91.In
second row C should deleted because it has less than 91 score in col V10.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
97
Can you please tell me the solution.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London V7 V8 V9 V10
0 1 G`
0 1 Ta
0 1 Ca
0 1 Aa
0 1 G_
0 1 GZ
0 1 C^
0 1 C\
0 1 AZ
97
Can you please tell me the solution.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
____
From: Bansal, Vikas
Sent: Friday, July 08, 2011 9:15 PM
To: r-help@r-project.org; dwinsem...@comcast.net
Subjec
c(90, 96, 92)
0 1 T94
0 1 C97
Can you please tell me the solution.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
argument should be a character vector of length 1
all but the first element will be ignored
and it is converting only the value in first row.How can I do this for all rows
in my data frame.
Please help me.I am new user for R.I will be very thankful to you.
Thanking you,
Warm Regards
Vikas B
ly above
the column.
What should I do.Please help me.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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0 -1 -1
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: wootten.adrie...@gmail.com [wootten.adrie...@gmail.com] On Behalf Of
Adrienne Wootten [amwoo...@ncsu.edu]
Sent: Tuesday, July 05, 2011 4:49 PM
To: B
not(as.character(m1[,1]) == as.character(m2[,1]),
all.equal(m1[, -1], m2[, -1][ names(m1)[-1] ]),
dim(merge(m1, m2, by = integer(0))) == c(36, 10))
Can you tell me what this code will do
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
__
Yes sir.I have already looked at merge()
but as I am new to R,I was not able to understand the argument that how should
i create a code for the logic i gave in previous mail .
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
135344116
135344118
these values are common in both input dataframes.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: David Winsemius [dwinsem...@comcast.net]
Sent: Monday, July 04, 2011 12:11 AM
To
please tell me how to code for this problem?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: David Winsemius [dwinsem...@comcast.net]
Sent: Monday, July 04, 2011 2:02 AM
To: Bansal, Vikas
Cc: Dennis Murphy; r-help@r
From: David Winsemius [dwinsem...@comcast.net]
Sent: Sunday, July 03, 2011 7:08 PM
To: Bansal, Vikas
Cc: Dennis Murphy; r-help@r-project.org
Subject: Re: [R] For help in R coding
On Jul 3, 2011, at 1:07 PM, Bansal, Vikas wrote:
> Yes you are ri
rather than if condition?
From: David Winsemius [dwinsem...@comcast.net]
Sent: Sunday, July 03, 2011 3:57 AM
To: Bansal, Vikas
Cc: Dennis Murphy; r-help@r-project.org
Subject: Re: [R] For help in R coding
On Jul 2, 2011, at 4:46 PM, Bansa
t", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )),
N = unlist(sapply(gregexpr("\\,|\\.", txtvec), function(x) if ( x[[1]] != -1)
length(x) else 0 )))
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
___
NK THIS CODING SEEMS TO BE GOOD
BUT I AM MISSING SOMETHING.
FOR YOUR CONVENIENCE I HAVE ATTACHED MY Case2.pileup file.
I AM VERY THANKFUL TO YOU AND APPRECIATE THAT YOU ARE HELPING AND TAKING YOUR
PRECIOUS TIME.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
__
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: David Winsemius [dwinsem...@comcast.net]
Sent: Saturday, July 02, 2011 6:19 PM
To: Bansal, Vikas
Cc: r-help@r-project.org
Subject: Re: [R] For help in R coding
On Jul 2
p as rownames, which was a
> surprise.
>
> If you wanted to count "A" and "a" as equivalent, then the split
> argument should be "a|A"
>
>
>>AS YOU MENTIONED THAT IF I WANT TO COUNT A AND a I SHOUL
ected ')' in "length)"
> length) , "-", 1)),T = unlist(lapply( lapply( sapply(mydf[,5], strsplit,
> split="t|T"),
Error: unexpected ')' in "length)"
What should I do?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings Coll
.$,.,
+a,g,,t,
+,.,^!.
+,$.,."
but how I should input my data(in column 9) from dataframe mydf using txt
command because there are thousands of rows?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
___
0 0
1 0 0 0
0 0 0 3
This output is for first 5 rows from the example given above.
I am new to R can you please help me.I will be very thankful to you.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
__
R
r plotting bar plot of defect codes based on
total cost. Is there a way to accomplish Pareto Chart, may be through
couple of stages?
Any help is appreciated.
Regards
Vikas Garud
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https://stat.ethz.ch/mailman/listinfo/r-
> A good place would be r-sig-gui. Regards
> Liviu
>
Thanks Liviu. Subscribing to that list.
Hope, it is still OK to write mails on these lists as well.
Regards
Vikas Garud
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version of RKward should solve the problem.
Thank you everybody for all the help. I'll be asking questions about
various tools that I would like to deploy through GUI's for R. I'll
also be sharing my experiences.
Vikas Garud
__
R-help@r
> lib="/home/vikas/R/i686-pc-linux-gnu-library/2.13", dependencies=TRUE)
also installing the dependencies ‘rJava’, ‘JavaGD’, ‘iplots’
* installing *source* package ‘rJava’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking wh
nd R console combination. Used Rkward to load the data
and set it active. In R console I used
boxplot(formula=Time~Distance+Transporter+Tonnage, data=Transportation.Time).
Resultant output (attached to this mail) is the best equivalent
output. I will be able to use this output in trai
tried to search the mailing list on box plot, but could not find
anything relevant. I have also searched in manual and seen this type
(or even more complex analysis) being done on terminal. However, I
need to do it under (any) GUI. Any help is highly appr
if X is a binomial variate with parameters n and p, find E[1/(X+1)]
--
View this message in context:
http://r.789695.n4.nabble.com/statistics-tp3437152p3437152.html
Sent from the R help mailing list archive at Nabble.com.
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Is there any way to include comments in the html output of R2HTML? Or
is there any other function in any package that produces an html
output including comments, commands and output of the commands.
Vikas Rawal
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rnorm(20))->b3
c(rep(1,10),rep(2,10))->b3$Phase
qplot(Year,CDR,data=b3,colour=Phase,geom=c("point","line"),gpar(legend.position="bottom"))->p
p+scale_colour_gradient2(limits=c(1,2),
midpoint=1.5,low="magenta",high="darkblue",bre
,data=b3,colour=Phase,geom=c("point","line"),legend.position="bottom")->p
p+scale_colour_gradient2(limits=c(1,2), midpoint=1,low="magenta",
mid="magenta", high="darkblue",breaks=c(1,2),labels=c(&q
()
pushViewport(viewport(height=0.4, width=0.4, x=0.4, y=0.8))
print(p, newpage=FALSE, pretty=FALSE)
Is there some other way of doing "pretty=FALSE" in the new version of ggplot2?
Vikas Rawal
[[alternative HTML version deleted]]
_
> There is an integrate.xy in sfsmic. Limitations discussed there.
Also see trap.rule in Hmisc
Vikas
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there an efficient way to write this piece of code where I can get it
to run faster ?
If I do something similar in Excel, it is much faster. But I have to use R,
since this is a part of a bigger program.
Any help will be appreciated.
Thanks and Regards
Vikas
--
http://www.vikaskumar.org/
minutes to run.
Is there an efficient way to write this piece of code where I can get it
to run faster ?
If I do something similar in Excel, it is much faster. But I have to use R,
since this is a part of a bigger program.
Any help will be appreciated.
Thanks and Regards
Vikas
[[alt
This works for me.
melt(my.dat,id=c("indiv","covar.1","covar.2"))->my.dat.1
names(my.dat.1)[4:5]<-c("level","case.id")
melt(my.dat.1,id=c("indiv","level","case.id"))->my.dat.2
Vikas
___
You can also use ggplot and then add layers for each geom_line that
you want to add.
Vikas
>
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