I am trying to read data from a bedfile into R, but I lose the last two columns when the read.table function is applied.
My bedfile has 6 columns:
$ head CHX_clean_sorted_data_plus.bed chr1 630725 630752 SN1052:386:C9VFHACXX:1:1305:11494:98114#RB:GTGCC 50 + chr1 630728 630752 SN1052:386:C9VFHACXX:1:1116:5611:86646#RB:GAGTG 50 + chr1 630728 630751 SN1052:386:C9VFHACXX:1:1213:17960:21112#RB:TTAGA 50 + chr1 630728 630752 SN1052:386:C9VFHACXX:1:1312:11292:52265#RB:TCAAA 50 + chr1 634005 634030 SN1052:386:C9VFHACXX:1:1110:17705:92051#RB:GTGCG 50 + chr1 634337 634367 SN1052:386:C9VFHACXX:1:2102:4448:4217#RB:TTGGA 50 +
The final two columns are lost when I use read.table to read the data into R
a <- read.table("CHX_clean_sorted_data_plus.bed", sep="\t", blank.lines.skip=FALSE) dim(a)  144712 4 head(a) V1 V2 V3 V4 1 chr1 630725 630752 SN1052:386:C9VFHACXX:1:1305:11494:98114 2 chr1 630728 630752 SN1052:386:C9VFHACXX:1:1116:5611:86646 3 chr1 630728 630751 SN1052:386:C9VFHACXX:1:1213:17960:21112 4 chr1 630728 630752 SN1052:386:C9VFHACXX:1:1312:11292:52265 5 chr1 634005 634030 SN1052:386:C9VFHACXX:1:1110:17705:92051 6 chr1 634337 634367 SN1052:386:C9VFHACXX:1:2102:4448:4217
I would appreciate any insight into what is causing this and how to fix it.
See read.table does not read in all rows! for a potential solution. The problem in your case seems to be the '#' sign.
I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
Stealing the screenshot for future use since you have already done the effort :)
Don't forget to cite me then, every time you use it ;) Having this as a standard moderation answer would be convenient :-p
Since @Istvan has finally completed the ChIP-seq chapter in Biostars handbook he may have time to revisit our Biostars feature wish list.
Thanks so much for your help. This worked great!
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