CODEWITHSUNDEEP
rdataframer-rownames
rshraim
rshraim

Reputation: 15

how to edit row names in dataframe from list of lists?

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!

Upvotes: 0

Views: 493

Answers (3)

Joris Meys
Joris Meys

Reputation: 108583

The advice would be: store that information in an extra variable. You can NOT store non-unique rownames in a dataframe:

df <- data.frame(
  A = 1:3,
  B = 3:1
)
rownames(df) <- c("D","E","D")

gives:

Error in `row.names<-.data.frame`(`*tmp*`, value = value) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique value when setting 'row.names': ‘D’

So you could do: 

mydataframe$origin <- gsub("\\d_(S\\d{1})_.+", "\\1", rownames(mydataframe))

But you can't set that as rownames.

Upvotes: 1

Osdorp
Osdorp

Reputation: 320

Alternatively, using gsub with group capturing:

a <- c("6_S6_annotated_filtered.vcf.gz877", "7_S7_annotated_filtered.vcf.gz569")
gsub('[0-9]+_(S[0-9]+)_annotated_filtered.vcf.*',"\\1",a)
#[1] "S6" "S7"

Upvotes: 0

amonk
amonk

Reputation: 1795

I would use:

 library(stringr)
 str_extract(row.names(mydataframe),"S[0-9]")

Upvotes: 0

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