Question: How to convert a meta-analysis file from PLINK (.meta) to a .csv or.txt to be read into R?
0
gravatar for rkl
8 months ago by
rkl0
rkl0 wrote:

Hi,

I'm encountering issues with reading .meta files into R. I am assuming the file needs to be reformatted to a .csv or a .txt. Does anyone have any idea of how to convert the PLINK output for meta-analysis (plink.meta) to a file format readable by R?

Thanks!

plink R • 406 views
ADD COMMENTlink modified 8 months ago by zx87548.0k • written 8 months ago by rkl0
1

I suggest you provide some more details: Is the .meta file a text file? Pasting the first few lines of the .meta file might increase your chances of getting an answer.

ADD REPLYlink written 8 months ago by Fabio Marroni2.3k

its the default output of plink meta-analysis which is plink.meta (text file). When I try to import it into R it can't differentiate the columns.

CHR          BP            SNP  A1  A2   N           P        P(R)    BETA BETA(R)       Q       I

   1      751343     rs28544273   T   A   2      0.9359      0.6009 -0.0026 -0.0400  0.1193   58.80
   1      751488    rs200141114   D   I   1          NA          NA      NA      NA      NA      NA
   1      751756    rs143225517   T   C   2      0.9346      0.6014 -0.0026 -0.0397  0.1195   58.74
   1      752566      rs3094315   G   A   2      0.9665      0.6312  0.0012  0.0306  0.1445   53.03

Thanks

ADD REPLYlink modified 8 months ago by WouterDeCoster40k • written 8 months ago by rkl0

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:

101010 Button

ADD REPLYlink written 8 months ago by WouterDeCoster40k
3
gravatar for chrchang523
8 months ago by
chrchang5235.5k
United States
chrchang5235.5k wrote:

See the comments on converting spaces to tabs under https://www.cog-genomics.org/plink/1.9/other#tabspace .

ADD COMMENTlink written 8 months ago by chrchang5235.5k
3
gravatar for zx8754
8 months ago by
zx87548.0k
London
zx87548.0k wrote:

Please post the code you are using to read the meta file and R is failing, also add error/warning messages. Plink output is Fixed Width Format, which should be easily read using below commands:

read.table("meta.txt", header = TRUE)

Or using data.table, for faster reading:

data.table::fread("meta.txt")

If above fails, then maybe try to use read as fixed width file using read.fwf function, see below StackOverflow post for more info:

ADD COMMENTlink written 8 months ago by zx87548.0k
1

This is actually a better answer than the one I gave. (I was reposting my reply to the more specific query at https://groups.google.com/forum/#!topic/plink2-users/zbr6cW3LeyU .)

ADD REPLYlink written 8 months ago by chrchang5235.5k
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