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Error: invalid subscript #238

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CherryX727 opened this issue Aug 12, 2024 · 0 comments
Open

Error: invalid subscript #238

CherryX727 opened this issue Aug 12, 2024 · 0 comments

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@CherryX727
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Hi, thanks for your tools.
When I try to give annotion to my bed file of ATAC-Seq data, I used code of following.
peakAnno <- annotatePeak(Ascl1_1_peaks,TxDb=txdb,tssRegion=c(-3000, 3000), verbose=FALSE,addFlankGeneInfo=TRUE, flankDistance=5000,annoDb="org.Mm.eg.db")
But it always prompts the error like 'Error: invalid subscript'.
So I try to check my input file with head(peaks).

GRanges object with 6 ranges and 2 metadata columns:
seqnames ranges strand | V4 V5
|
[1] NC_000067.7 3051930 * | Ascl1-1_peak_1 5.22645
[2] NC_000067.7 3077661 * | Ascl1-1_peak_2 3.50514
[3] NC_000067.7 3264656 * | Ascl1-1_peak_3 4.34534
[4] NC_000067.7 3404048 * | Ascl1-1_peak_4 2.71066
[5] NC_000067.7 3431298 * | Ascl1-1_peak_5 7.09632
[6] NC_000067.7 3443044 * | Ascl1-1_peak_6 7.09632
.......
seqinfo: 33 sequences from an unspecified genome; no seqlengths

Is there any mistakes in my file, or how can I solve this problem?

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