I'm new to R (I've tried searching; sorry if this is repeated elsewhere!) and I need some help please! I'm trying to edit the row names in a data.frame:
I start with several vcf files and create a list of lists using lapply() then flatten the list using unlist() and combine the extracted indicators into a dataframe but I end up with the following:
> row.names(mydataframe)
[1] "1_S1_annotated_filtered.vcf.gz1" "1_S1_annotated_filtered.vcf.gz2" "1_S1_annotated_filtered.vcf.gz3" "1_S1_annotated_filtered.vcf.gz6"
[5] "1_S1_annotated_filtered.vcf.gz7" "1_S1_annotated_filtered.vcf.gz8"
...
[457] "6_S6_annotated_filtered.vcf.gz877" "6_S6_annotated_filtered.vcf.gz888" "6_S6_annotated_filtered.vcf.gz907" "7_S7_annotated_filtered.vcf.gz309"
[461] "7_S7_annotated_filtered.vcf.gz354" "7_S7_annotated_filtered.vcf.gz477" "7_S7_annotated_filtered.vcf.gz485" "7_S7_annotated_filtered.vcf.gz537"
[465] "7_S7_annotated_filtered.vcf.gz569" "7_S7_annotated_filtered.vcf.gz575" "7_S7_annotated_filtered.vcf.gz721" "7_S7_annotated_filtered.vcf.gz871"
[469] "7_S7_annotated_filtered.vcf.gz892" "8_S8_annotated_filtered.vcf.gz136" "8_S8_annotated_filtered.vcf.gz191" "8_S8_annotated_filtered.vcf.gz967"
whereas what I need is
> row.names(mydataframe)
[1] "S1" "S1" "S1" "S1"
[5] "S1" "S1" "S1" "S1"
....
[469] "S7" "S8" "S8" "S8"
Any advice? Thanks in advance!
I would use:
library(stringr)
str_extract(row.names(mydataframe),"S[0-9]")