Question

Split AME .tsv file into GRanges object or DataFrame

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rbronste ▴ 60

@rbronste-12189

Last seen 5.0 years ago

I have an AME motif calling output as follows (in a .tsv file) and can import this into R using read.table, however I would like to take the motif_ID, seq_ID, and class fields and split it off into a GRanges object or DataFrame, how can I go about doing this? Thanks!

motif_DB	motif_ID	seq_ID	FASTA_score	PWM_score	class
JASPAR2018_CORE_vertebrates	MA0004.1	chr8:3235975-3236325	146	11.6737	tp

meme ame motif dataframe granges • 1.4k views

ADD COMMENT • link updated 6.1 years ago by Michael Lawrence ★ 11k • written 6.1 years ago by rbronste ▴ 60

score 1 · Answer 1 · 2018-10-31

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.0 years ago

United States

gr <- GRanges(df$seq_ID)
mcols(gr) <- df[setdiff(colnames(df), "seq_ID")]

ADD COMMENT • link 6.1 years ago Michael Lawrence ★ 11k

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So after read.table, if I do as you suggest I get the following error:

> gr<- GRanges(t$seq_ID)
Error in .from_character_to_GRanges(from) : 
The character vector to convert to a GRanges object must contain strings of the form "chr:start-end" or "chr:start-end:strand", with end >=start - 1, or "chr:pos" or "chr:pos:strand". For example: "chr1:2501-2900", "chr1:2501-2900:+", or "chr1:740". Note that ".." is a valid alternate start/end separator. Strand can be "+", "-", "*", or missing.

Which is odd since my seq_ID column does match the format it specifies.

ADD REPLY • link 6.1 years ago rbronste ▴ 60