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ERROR- one SNP in one biofeature per one risk tagSNP? #18

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suhnrhie opened this issue Nov 14, 2011 · 0 comments
Open

ERROR- one SNP in one biofeature per one risk tagSNP? #18

suhnrhie opened this issue Nov 14, 2011 · 0 comments

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@suhnrhie
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I am running the newest version of FunciSNP(source the .R file from gitfolder), and error occurred... T,T

The new FunciSNP folder is here,
/media/bigboy/suhn/New_FunciSNP/

bed files are in the sub-folder, bed_files/
/media/bigboy/suhn/New_FunciSNP/bed_files

Basically, error occurred after scanning all biofeatures in all ethnic groups for the first risk tag SNP.
I guess when the second risk tag SNP, rs2981579 is used to scan with first biofeature, Enhancer_HMEC_CTCF_hg19.bed, the error seems to occur due to data lines?

This is the error message.

Pulling In Variants File for SNP: rs2981579
trying ncbi as 1000 genomes server
OK using ncbi : ftp://ftp-trace.ncbi.nih.gov/1000genomes/
[get_local_version] downloading the index file...
subsetting Variants File for racial/ethnic group: AFR
time: 12:02:42 Risk SNP: rs2981579, AFR (2/56)

(1/13) Enhancer_HMEC_CTCF_hg19.bed
Error in $<-.data.frame(*tmp*, "loc.feature", value = c("chr10:123813382-123814049", :
replacement has 177 rows, data has 173
In addition: There were 50 or more warnings (use warnings() to see the first 50)

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