Calculate number of overlapped extended reads per nucleotide position

Description

Calculate number of overlapped extended reads per nucleotide position

Usage

mappedReads2Nhits(input, file , chr = c("chr1", "chr2", "chr3", "chr4", "chr5"), chrL = "TAIR9", w = 300L, considerStrand = "Minimum", uniquelyMapped = TRUE, uniquePosition = FALSE)

Arguments

Value

A list to be used for other functions of the CSAR package

Author(s)

Jose M Muino, jose.muino@wur.nl

References

Muino et al. (submitted). Plant ChIP-seq Analyzer: An R package for the statistical detection of protein-bound genomic regions.
Kaufmann et al.(2009).Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biology; 7(4):e1000090.

See Also

CSAR-package

Examples

#For this example we will use the a subset of the SEP3 ChIP-seq data (Kaufmann, 2009)
data("CSAR-dataset");
#We calculate the number of hits for each nucleotide posotion for the sample. We do that just for chromosome chr1, and for positions from 1 bp to 10kb
nhitsS<-mappedReads2Nhits(sampleSEP3_test,file="sampleSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(CSAR)
Loading required package: S4Vectors
Loading required package: stats4
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 objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CSAR/mappedReads2Nhits.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mappedReads2Nhits
> ### Title: Calculate number of overlapped extended reads per nucleotide
> ###   position
> ### Aliases: mappedReads2Nhits mappedReads2Nhits_chr pos2Nhits
> ###   pos2Nhits_old
> 
> ### ** Examples
> 
> 
> #For this example we will use the a subset of the SEP3 ChIP-seq data (Kaufmann, 2009)
> data("CSAR-dataset");
> #We calculate the number of hits for each nucleotide posotion for the sample. We do that just for chromosome chr1, and for positions from 1 bp to 10kb
> nhitsS<-mappedReads2Nhits(sampleSEP3_test,file="sampleSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000))
mappedReads2Nhits has just finished   CHR1v01212004 ...
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>