Sorting Enhancers According To Transcription Factors In R
Hi everyone,
I have a file like this with enhancers from 4 different genes with their TFs:
gene1 gene2 gene3 gene4 TF
gene1Enhancer1 gene2Enhancer1 gene3Enhancer2 Gene4Enhancer1 V$GSH1
gene1Enhancer2 gene2Enhancer2 gene3Enhancer3 Gene4Enhancer2 V$GSH1
gene1Enhancer3 gene2Enhancer3 gene3Enhancer4 Gene4Enhancer3 V$GSH1
gene1Enhancer1 gene2Enhancer1 gene3Enhancer2 Gene4Enhancer1 V$REF
gene1Enhancer3 gene2Enhancer3 gene3Enhancer4 Gene4Enhancer3 V$AB
gene1Enhancer6 gene2Enhancer6 gene3Enhancer7 Gene4Enhancer6 V$LEF1
I want the output to be sorted such that the first 4 columns are sorted so that same enhancers from 4 columns are put together with their transcription factors so it should look like this:
gene1 gene2 gene3 gene4 TF
gene1Enhancer1 gene2Enhancer1 gene3Enhancer2 Gene4Enhancer1 V$GSH1
gene1Enhancer1 gene2Enhancer1 gene3Enhancer2 Gene4Enhancer1 V$REF
gene1Enhancer3 gene2Enhancer3 gene3Enhancer4 Gene4Enhancer3 V$GSH1
gene1Enhancer3 gene2Enhancer3 gene3Enhancer4 Gene4Enhancer3 V$AB
gene1Enhancer2 gene2Enhancer2 gene3Enhancer3 Gene4Enhancer2 V$GSH1
gene1Enhancer6 gene2Enhancer6 gene3Enhancer7 Gene4Enhancer6 V$LEF1
I was thinking of using aggregate function in R but that didn't help. Any advice?
Thanks a lot!!!
• 2,127 views
•
link
updated
by
Anthony Mathelier
•
written
by
Diana
•
written
by
Diana
2 answers
Sorting example based on multiple columns:
m <- matrix( sample(1:5, 20, rep=TRUE), nc=2)
m[ order(m[,1],m[,2]), ]
Also have a look at this How to sort a dataframe by column(s) in R
Just in case you need it outside of R, only one line is necessary in your terminal:
$ sort -k4,4 [input file] > [output file]
• 0 views
•
link
written
by
Anthony Mathelier
Log in to answer this question.