Hi people,
I have a text file like this one posted:
snp_id gene chromosome distance_from_gene_center
position pop1 pop2 pop3 pop4 pop5 pop6 pop7
rs2129081 RAPT2 3 -129993 "upstream" 0.439009
1.169210 NA 0.233020 0.093042 NA
-0.902596
rs1202698 RAPT2 3 -128695 "upstream" NA
1.815000 NA 0.399079 1.814270 1.382950
NA
rs1163207 RAPT2 3 -128224 "upstream" NA NA
NA NA NA NA NA
rs1834127 RAPT2 3 -128106 "upstream" NA NA
NA NA NA NA 2.180670
rs2114211 RAPT2 3 -126738 "upstream" -0.468279
-1.447620 NA 0.010616 -0.414581 NA
0.550447
rs2113151 RAPT2 3 -124620 "upstream" -0.897660
-1.971020 NA -0.920327 -0.764658 NA
0.337127
rs2524130 RAPT2 3 -123029 "upstream" -0.109795
-0.004646 -0.412059 1.116740 0.667567
-0.924529 0.962841
rs1381318 RAPT2 3 -12818 "upstream" -0.911662
-1.791580 NA -0.945716 -1.239640 NA
0.004876
rs2113319 RAPT2 3 -122028 "upstream" -0.911662
-1.738610 NA -0.945716 -1.240950 NA -0.005318
When I use read.delim (or any read function) on it, R skips the first
column, and I don' understand why.
For example:
$: R
> data = read.delim('snp_file.txt', head=T, sep='\t')
Now, I would expect data$snp_id to contain snp ids, and data$gene to contain
gene names; but it is not like this:
> data$snp_id
[1] RAPT2 RAPT2 RAPT2 RAPT2 RAPT2 RAPT2 RAPT2 RAPT2 RAPT2
Levels: RAPT2
> data$gene
[1] 3 3 3 3 3 3 3 3 3
> summary(data)
snp_id gene chromosome distance_from_gene_center
RAPT2:9 Min. :3 Min. :-129993 upstream:9
1st Qu.:3 1st Qu.:-128224
Median :3 Median :-126738
Mean :3 Mean :-113806
3rd Qu.:3 3rd Qu.:-123029
Max. :3 Max. : -12818
....
> data$pop7
[1] NA NA NA NA NA NA NA NA NA
Notice that it did use snp_id as the header for the first column, but it
skips completely al the data from that column, and all the fields are
shifted, so the last column is filled with NA values.
What I am doing wrong? Can it be a problem of my data files? I have tried to
modify them a bit (add new columns, etc..) but it didn't work.
I am running R from an Ubuntu system:
> sessionInfo()
R version 2.9.1 (2009-06-26)
i486-pc-linux-gnu
locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
My blog on bioinformatics: http://bioinfoblog.it
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