How to subset data with advance string matching

Question

I have the following data frame from which I would like to extract rows based on matching strings.

> GEMA_EO5
gene_symbol  fold_EO  p_value                            


        

Answer 1

To do partial matching you'll need to use regular expressions (see ?grepl). Here's a solution to your particular problem:

##Notice that the first element appears in 
##a row containing commas
l = c( "NM_013433", "NM_001386", "NM_020385")

To test one sequence at a time, we just select a particular seq id:

R> subset(GEMA_EO5, grepl(l[1], GEMA_EO5$RefSeq_ID))
  gene_symbol fold_EO p_value                           RefSeq_ID BH_p_value
5       TNPO2   4.708 1.6e-23 NM_001136195,NM_001136196,NM_013433  1.538e-20

To test for multiple genes, we use the | operator:

R> paste(l, collapse="|")
[1] "NM_013433|NM_001386|NM_020385"
R> grepl(paste(l, collapse="|"),GEMA_EO5$RefSeq_ID)
[1] FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE

So

subset(GEMA_EO5, grepl(paste(l, collapse="|"),GEMA_EO5$RefSeq_ID))

should give you what you want.