select unique samples in R

Question

[Bioinfonext]

Hi all,

Here are two data frame list1 has 1483 samples and list2 has 1928 samples. Could you please help how to extract those Sample_ID which are only present in list2 as shown below but not in list1.

   list1 <- read.table("phe_nodiab_051223.txt", header=T, sep="\t", a> is=T, na.strings="NA")
 > head(list1)
     Sample_ID          BeadChipID  Sentrix_ID Sentrix_Position Batch
1   1.872 200772310035_R08C01 2.00772e+11           R08C01     3
2   1.818 200793300045_R02C01 2.00793e+11           R02C01    20
3   1.492 200788240034_R04C01 2.00788e+11           R04C01    20
4   1.072 200772280022_R08C01 2.00772e+11           R08C01     1
5  
> list2 <- read.table("Phe_121023.csv", header=T, sep=",", as.is=T, n> strings="NA")
> head(list2)
    Sample_ID         BeacChip.ID   Sentrix_ID Sentrix_Position Batch
1 1.093 200772280026_R05C01 200772280026           R05C01    16
2 1.095 200772280026_R07C01 200772280026           R07C01    16
3 1.096 200772280026_R08C01 200772280026           R08C01    16
4 1.097 200772280027_R01C01 200772280027           R01C01    16
5 1.098 200772280027_R02C01 200772280027           R02C01    16
6 1.100 200772280027_R04C01 200772280027           R04C01    16

> dim(list2)
[1] 1928   19
> dim(list1)
1483   21

[ATpoint]

setdiff() -- from here on make it a learning experience and just try things.

[Bioinfonext]

thanks a lot, it work very well, what about if I need to extract whole data frame;

> #find differences between the points columns in the two data frames
> setdiff(list1$Sample_ID, list2$Sample_ID)

[Matthias Zepper]

Then you use the resulting IDs to subset your original data frame(s).

[bk11]

Instead of setdiff(list1$Sample_ID, list2$Sample_ID) do this-

setdiff(list1, list2)