Say I have a tab-delimited table I want to read into R. What should I
expect to happen if some of the entries contain the character " ' "? I
thought it would read the file fine, but that is not what happens.
Instead, all the values in between two " ' "s get read into one field,
and things are just seriously messed up. Is this a bug, and besides
removing the offending characters, is there a fix?
Example Input file:
testFile.txt:
3499 9031 424823 COP'B2 118094989 XP_422637.2
3499 7955 114454 copb2 50080158 NP_001001940.1
3499 7227 45757 betaCop 24584107 NP_524836.2
3499 7165 1278426 AgaP_AGAP004798 158297839 XP_318012.4
3499 6239 177779 F38E11.5 17540286 NP_501671.1
3499 4896 2540050 sec'27 19113604 NP_596811.1
3499 4932 852740 SEC27 6321301 NP_011378.1
3499 28985 2897447 KLLA0B01958g 50303353 XP_451618.1
3499 33169 4621659 AGOS_AFL118W 45198403 NP_985432.1
3499 148305 2682116 MGG_10504 145615762 XP_366285.2
3499 5141 2709504 NCU07319.1 32414251 XP_327605.1
3499 3702 820842 AT3G15980 30683862 NP_850592.1
3499 3702 841666 AT1G52360 15218215 NP_175645.1
3499 3702 844339 AT1G79990 30699476 NP_178116.2
3499 4530 4340097 Os06g0143900 115466360 NP_001056779.1
testDat <- read.table('testFile.txt',sep='\t')
testDat
V1 V2 V3
1 3499 9031 424823
2 3499 4932 852740
3 3499 28985 2897447
4 3499 33169 4621659
5 3499 148305 2682116
6 3499 5141 2709504
7 3499 3702 820842
8 3499 3702 841666
9 3499 3702 844339
10 3499 4530 4340097
V4
1
COPB2\t118094989\tXP_422637.2\n3499\t7955\t114454\tcopb2\t50080158\tNP_001001940.1\n3499\t7227\t45757\tbetaCop\t24584107\tNP_524836.2\n3499\t7165\t1278426\tAgaP_AGAP004798\t158297839\tXP_318012.4\n3499\t6239\t177779\tF38E11.5\t17540286\tNP_501671.1\n3499\t4896\t2540050\tsec27
2
SEC27
3
KLLA0B01958g
4
AGOS_AFL118W
5
MGG_10504
6
NCU07319.1
7
AT3G15980
8
AT1G52360
9
AT1G79990
10
Os06g0143900
V5 V6
1 19113604 NP_596811.1
2 6321301 NP_011378.1
3 50303353 XP_451618.1
4 45198403 NP_985432.1
5 145615762 XP_366285.2
6 32414251 XP_327605.1
7 30683862 NP_850592.1
8 15218215 NP_175645.1
9 30699476 NP_178116.2
10 115466360 NP_001056779.1
I would appreciate any feedback.
Thanks,
-Robert
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.12.1
Robert M. Flight, Ph.D.
University of Louisville Bioinformatics Laboratory
University of Louisville
Louisville, KY
PH 502-852-1809 (HSC)
PH 502-852-0467 (Belknap)
EM robert.fli...@louisville.edu
EM rfligh...@gmail.com
Williams and Holland's Law:
If enough data is collected, anything may be proven by
statistical methods.
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