[R] Removing the rows where all the elements are 0

[arun]

Hi Vivek,

dat1<- read.table(text="
gene    ZPT.1   ZPT.0   ZPT.2   ZPT.3   PDGT.1  PDGT.0
XLOC_000001 3516    626 1277    770 4309    9030
XLOC_000002 342 82  185 72  835 1095
XLOC_000003 2000    361 867 438 454 687
XLOC_000004 143 30  67  37  90  236
XLOC_000005 0   0   0   0   0   0
XLOC_000006 0   0   0   0   0   0
XLOC_000007 0   0   0   0   1   3
XLOC_000008 0   0   0   0   0   0
XLOC_000009 0   0   0   0   0   0
XLOC_000010 7   1   5   3   0   1
XLOC_000011 63  10  19  15  92  228
",sep="",stringsAsFactors=FALSE,header=TRUE)

res<- dat1[rowSums(dat1[,-1]==0)!=(ncol(dat1)-1),]
res
#          gene ZPT.1 ZPT.0 ZPT.2 ZPT.3 PDGT.1 PDGT.0
#1  XLOC_000001  3516   626  1277   770   4309   9030
#2  XLOC_000002   342    82   185    72    835   1095
#3  XLOC_000003  2000   361   867   438    454    687
#4  XLOC_000004   143    30    67    37     90    236
#7  XLOC_000007     0     0     0     0      1      3
#10 XLOC_000010     7     1     5     3      0      1
#11 XLOC_000011    63    10    19    15     92    228

If it is a matrix:
mat1<- as.matrix(dat1[,-1])
 row.names(mat1)<- dat1[,1]


 res2<-mat1[rowSums(mat1==0)!=ncol(mat1),]
 res2
#            ZPT.1 ZPT.0 ZPT.2 ZPT.3 PDGT.1 PDGT.0
#XLOC_000001  3516   626  1277   770   4309   9030
#XLOC_000002   342    82   185    72    835   1095
#XLOC_000003  2000   361   867   438    454    687
#XLOC_000004   143    30    67    37     90    236
#XLOC_000007     0     0     0     0      1      3
#XLOC_000010     7     1     5     3      0      1
#XLOC_000011    63    10    19    15     92    228


#I don't have an account in stackoverflow.  So, it is must be somebody else.
A.K.


________________________________
From: Vivek Das <vd4mmind at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Monday, August 5, 2013 6:31 AM
Subject: Removing the rows where all the elements are 0



Hi Arun,
Am using a matrix of gene expression, frag counts to calculate differentially expressed genes. I would like to know how to remove the rows which have values as 0. Then my data set will be compact and less spurious results will be given for the downstream analysis I do using this matrix.
Input
gene    ZPT.1ZPT.0ZPT.2ZPT.3PDGT.1PDGT.0XLOC_000001 3516626127777043099030XLOC_000002 34282185728351095XLOC_000003 2000361867438454687XLOC_000004 14330673790236XLOC_000005 000000XLOC_000006 000000XLOC_000007 000013XLOC_000008 000000XLOC_000009 000000XLOC_000010 715301XLOC_000011 6310191592228
Desired output
gene    ZPT.1ZPT.0ZPT.2ZPT.3PDGT.1PDGT.0XLOC_000001 3516626127777043099030XLOC_000002 34282185728351095XLOC_000003 2000361867438454687XLOC_000004 14330673790236XLOC_000007 000013XLOC_000010 715301XLOC_000011 6310191592228
As of now I only want to remove those rows where all the frag count columns are 0 if in any row some values are 0 and others are non zero I would like to keep that row intact as you can see my example above.
Please let me know how to do this.

 Hey arun I did not understand the command you wrote in the R stack overflow forum can you plase write here and help me out.
----------------------------------------------------------

Vivek Das
PhD Student in Computational Biology
Giuseppe Testa's Lab
European School of Molecular Medicine
IFOM-IEO Campus
Via Adamello, 16
Milan, Italy

emails: vivek.das at ieo.eu
            vchris_05 at yahoo.co.in
            vd4mmind at gmail.com