I am trying to run csaw but I am getting the following error:
Error: could not find function "normOffsets".
I could not see it either in the functions available.
> library(csaw)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unlist, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Loading required package: IRanges
Loading required package: GenomeInfoDb
> ?norm
?norm ?normalizePath
?normalize ?normalizeSingleBracketReplacementValue
?normalize,SummarizedExperiment-method ?normalizeSingleBracketReplacementValue,ANY-method
?normalizeCounts ?normalizeSingleBracketSubscript
?normalizeDoubleBracketSubscript
One thing I did is to copy paste the entire function from github https://github.com/Bioconductor-mirror/csaw/blob/master/R/normOffsets.R
and it seems to be working.