I am attempting to use BayesPeak. I have a file of mapped reads from a ChIP-seq experiment and from a negative control in bed6 format.
The following is my output:
library(BayesPeak) > raw.output <- bayespeak("chip.bed", "negative.bed", chr = "chr", start = 80000, end = 100000, job.size = 1000) Read 23148733 records Read 21898540 records [0% done] Starting chr:80000-1e+05:Error in var(tr$"+"$norm[x:x]) : error in evaluating the argument 'x' in selecting a method for function 'var': Error in tr$"+"$norm[x:x] : only 0's may be mixed with negative subscripts
I am not sure what is causing this error. Does anyone have some insight into this? I have pasted my session info below.
> sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  BayesPeak_1.12.0 IRanges_1.20.4 BiocGenerics_0.8.0 loaded via a namespace (and not attached):  stats4_3.0.2