mappedReads2Nhits: Calculate number of overlapped extended reads per nucleotide...
In CSAR: Statistical tools for the analysis of ChIP-seq data

Description Usage Arguments Value Author(s) References See Also Examples

Calculate number of overlapped extended reads per nucleotide position

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

`input`	data loaded with loadMappedReads or an AlignedRead object from the ShortRead package
`file`	Name of the file where the results will be saved. If NA the results will not be saved in a file.
`chr`	Character vector containing the chromosome names as identified on `input`.
`chrL`	Numeric vector containing the length (bp) of the chromosomes. It should be in the same order than `chr`
`w`	Integer corresponding to the desired length of the extended reads. An advised value will be the average fragment length of the DNA submitted to sequence (usually 300 bp).
`considerStrand`	Character value. "Minimum"=>Default value. Report the minimum number of hits at each nucleotide position for both strands. "Foward"=> Report the number of hits at each nucleotide position for the "foward" strands (the one denoted as "+" in `q`). "Reverse"=>Report the number of hits at each nucleotide position for the "reverse" strands (the one denoted as "-" in `q`). "Sum"=>Report the sum of number of hits at each nucleotide position for both strands.
`uniquelyMapped`	Logic value, If TRUE, only consider uniquely mapped reads.
`uniquePosition`	Logic value. If TRUE, only consider reads mapped in different positions.

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

`chr`	Chromosme names
`chrL`	Chromosme length (bp)
`chrL_0`	Number of nucleotide positions with at least one extended read
`chrL_0`	Number of nucleotide positions with at least one extended read
`filenames`	Name of the files where the Nhits values are storaged
`c1`	Sum of all the Nhits values for each chromosome
`c2`	Sum of all the Nhits square values for each chromosome

Jose M Muino, jose.muino@wur.nl

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.

CSAR-package

#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))