mappedReads2Nhits: 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

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

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.

Value

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

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.

Examples

Run this code


#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))