Using Custom Bed File

[Akinola Emmanuel]

I'm trying to use a custom bed file as my region for plotting, but I receive the following error message:

Configuring variables...Error in if (!all(genome.coord$start <= genome.coord$end)) { : 

  missing value where TRUE/FALSE needed

Calls: SetupPlotCoord -> ReadBedCoord

In addition: Warning messages:

1: In Ops.factor(bed.coord[, 2], 1) : ‘+’ not meaningful for factors

2: In Ops.factor(genome.coord$start, genome.coord$end) :

  ‘<=’ not meaningful for factors

Execution halted

I suspect it's a problem with R, but I'm not sure. I'm using NGSPLOT 2.47.1 and R 3.2.0 on a MAC running version 10.10.2 of OSX Yosemite. The command that I run is 

ngs.plot.r -G mm9 -R bed -C WT_sorted.bam -O WT_analysis.txt -E WT_peaks.bed

Thanks.

[Li Shen]

What does your custom bed file look like? Here are some instructions on creating bed files:

https://github.com/shenlab-sinai/ngsplot/wiki/HowToCreateBed

Li

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Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
New York, NY 10029
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