This is a very simple question.
I have a lengthy dataset and want to create a subset based on certain entries in a particular column. In this case, I am setting it up like this:
Example data:
> NL
SNP alleles
rs1234 A_T
rs1235 A_G
rs2343 A_T
rs2342 G_C
rs1134 C_G
rs1675 T_A
rs8543 A_T
rs2842 G_A
P <- subset(NL, alleles = "A_T", alleles = "T_A", alleles = "G_C", alleles = "C_G")
This runs without error, but the resulting P is not subset in any way (tail of P still shows same number of entries as original NL).
What am I doing wrong?
The most obvious error is using "=" when you mean"==". But I'm guessing from context that you really want to "split" this data:
split(NL, NL$alleles)
Which will create a list of dataframes each of which has one of the values for alleles.
But perhaps you do want to use pattern matching:
NL[ grepl("C_G|G_C|A_T|T_A", NL$alleles), ]
SNP alleles
1 rs1234 A_T
3 rs2343 A_T
4 rs2342 G_C
5 rs1134 C_G
6 rs1675 T_A
7 rs8543 A_T
And illustrating with what I think was your comment-example:
P <- read.table(text="V1 V2 V3 V4 V5 V6 alleles
15116 25 rsX 0 123412 G A G_A
15117 25 rsX1 0 23432 A C A_C
15118 25 rsX2 0 234324 A G A_G
15119 25 rsX3 0 3423 A G A_G
15120 25 rsX4 0 2343223 C A C_A
15121 25 rsX5 0 23523423 A G A_G", header=TRUE)
P[ grepl("G_A", NL$alleles), ]
# V1 V2 V3 V4 V5 V6 alleles
# 15116 25 rs306910 0 154613671 G A G_A
The subset version:
subset(P, alleles %in% c("G_A", "A_G") )
V1 V2 V3 V4 V5 V6 alleles
15116 25 rsX 0 123412 G A G_A
15118 25 rsX2 0 234324 A G A_G
15119 25 rsX3 0 3423 A G A_G
15121 25 rsX5 0 23523423 A G A_G