Re: [R] collapse a data column into a row

here name IN (" , idListWithSep , ") ", sep ='') 1> query [1] "select * from rat_rn4_affy_RG_U34Cprobe_fasta where name IN ('rc_AI104113_at','rc_AI178259_f_at','rc_AI179134_i_at','rc_AI179134_f_at','rc_AI104113_at','rc

[R] collapse a data column into a row

_i_at', 'rc_AI179134_f_at', 'rc_AI104113_at', 'rc_AA819429_f_at' Is there any function to do this. I can do it by using iterative paste but I just want to avoid it for efficiency reason as number of probes is very high. Thanks --Fahim [[alternative HTML version dele

[R] RCytoscape setPosition error

capeRPC.CytoscapeRPCCallHandler: null setPosition(cw, nodesTo , c(600, 600, 600), c(100, 200, 300)) Error in convertToR(xmlParse(node, asText = TRUE)) : faultCode: 1001 faultString: Node with id: D could not be found. Thanks --Fahim [[alternative HTML version deleted]] ___

[R] Layout control from RCytoscape

. / / a1 --- / \ a -a2 \ \a3 / a4 / b a5 \ \ a6 .. ... Can I draw this type of graph from Rcytoscape. Thanks Fahim -- Fahim Mohammad Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167

[R] bit wise operation on long bit vector?

01100.." "c" "000..." "dd" "0000.." Thanks -- Fahim Mohammad Bioinforformatics Lab University of

Re: [R] problem reading file containing bit vector

Its working now. I was missing something. dataFile = read.table("./Data/occTable.csv", sep ='\t', header=TRUE, colClasses = "character"); i=1 x = dataFile[i,]; x Thanks a lot. On Sun, Jan 30, 2011 at 12:25 PM, David Winsemius wrote: > > On Jan 30, 2011, a

[R] problem reading file containing bit vector

;Inf" . How should i read this file? as.is/colclasses field in read function is not helping me. Is there any package that can do bitwise operation(and/or) on bitVectors. bitops seems to do that but I need output in bitvector format only. Thank

[R] multicore package: help

I have matrices as below: a <- matrix(c(1:10, 11, 12), 3,4) aa <- data.frame(a) b <- matrix(c(10:20, 21), 4,3) bb <- data.frame(b) ... and many more matrices. st = list(aa,bb, . ) mclapply(st, FUN, mc.cores=6); #this function apply the function to the elements of the list 'aa', 'bb'...etc

[R] How to access values in s4 method

Hi How to access the values in the output that is an object of S4 type. I tried to access using subset ( [ ] ) but it is not allowed. Any clue?? Thanks -- Fahim #My code is as follows: require(IRanges); query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2,

[R] union data in column

col3col4 G234064 1 1 0 0 // 1 appears in col1 and col2 above, rest are zero G234065 0 1 1 1 // 1 appears in col2 , 3 and 4 above. Thanks -- Fahim

Re: [R] calling a c function from R

of); } fclose(fr); fclose(of); } -- Thats it! I saved almost a week in parsing all those genbank est files(almost 413 files). Thanks R&C interface team. --Fahim On Wed, Jul 14, 2010 at 10:18 AM, Matt Shotwell wrote: > Fahim,

[R] calling a c function from R

puts( "Output file not given.\n" ); } } else {printf("wrong usage: Try Agay!!! correct usage is:= functionName inputfileToParse outFileToWriteInto\n"); } while(fgets(line, 81, fr) != NULL) -- --- -- } Thanks again Fahim --

[R] Is there any function to read genbank flat files.

iliar with python functions so I want to avoid that and I am keeping it as last resort) Thanks and regards. --Fahim -- Fahim Mohammad Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167 [[alternative HTML versi

[R] installing a package in linux

, I just need to put require('package-name') to use its function). Is there anyway so that reinstallation of the package is avoided??? thanks --Fahim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.e

[R] using BLAT in r

on or some material that addresses such problem. Help appreciated. Thanks -Fahim Mohammad cecs, univ of Louisville -- View this message in context: http://n4.nabble.com/using-BLAT-in-r-tp1835763p1835763.html Sent from the R help mailing list archive at

Re: [R] selecting certain columns or rows from a .csv

to select rows and col simultaneously as specified above then modifiedDataFile = dataFile[c(1:100, 1000:5000), c(col1, col9, col15)]; Hope this will work. Thanks Fahim Mohammad Grad student CECS, Univ of Louisville -- View this message in context: http://n4.nabble.com/selecting-certain-

[R] using BLAT in r

Does anyone know how to use BLAT(Blast-Like alignment tool) in R? Thanks and regards. -- Fahim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] strange behavior of R

quot;y1" > arr[2] [1] "y2" I think, when there is single row, R is considering it as an array and not as matrix. But why it is so?/ -Fahim -- View this message in context: http://n4.nabble.com/strange-behavior-of-R-tp1010047p1010047.html Sent from the R help mailing

[R] variable three dimensional array

this regard will be highly appreciated. thanks ---Fahim Louisville, KY, USA [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

[R] PRoblem with paste function

I am having trouble with paste function. I dont know how to proceed. I tried many options but i failed miserably. I am using a variable f1 to assign a string as below: f1=dataLine[locAffyProbeID]; ( the value of f1 is 244901_at ) Then I am using the paste function paste("set @g1=", f1); in

[R] problem with paste function

set g=", f1); instead of getting *set g=244901_at*, I am getting *set g=23*. I am not able to understand why it is so. Can anyone help!!!Please.. Thanks -- Mohammad Fahim [[alternative HTML version deleted]] __ R-help@r-project.org ma

[R] PRoblem with paste function

Hi there!!! I am having trouble with *paste* function. I dont know how to proceed. I tried many options but i failed miserably. I am using a variable f1 to assign a string as below: f1=dataLine[locAffyProbeID]; ( the value of f1 is *244901_at* ) Then I am using the paste function paste("set @g