Statistical tools for the analysis of ChIP-seq data

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Documentation for package ‘CSAR’ version 1.56.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

CSAR-package	Statistical tools for the analysis of ChIP-seq data
ChIPseqScore	Calculate read-enrichment scores for each nucleotide position
controlSEP3_test	Partial dataset of a ChIP-seq experiment
distance2Genes	Calculate relative positions of read-enriched regions regarding gene position
genesWithPeaks	Provide table of genes with read-enriched regions, and their location
getPermutatedWinScores	Obtain the read-enrichment score distribution under the null hypothesis
getThreshold	Calculate the threshold value corresponding to control FDR at a desired level
LoadBinCSAR	Save the read-enrichment scores at each nucleotide position in a .wig file format
loadMappedReads	Load mapped reads
mappedReads2Nhits	Calculate number of overlapped extended reads per nucleotide position
mappedReads2Nhits_chr	Calculate number of overlapped extended reads per nucleotide position
permutatedWinScores	Calculate scores for permutated read-enriched regions
pos2Nhits	Calculate number of overlapped extended reads per nucleotide position
pos2Nhits_old	Calculate number of overlapped extended reads per nucleotide position
sampleSEP3_test	Partial dataset of a ChIP-seq experiment
score2wig	Save the read-enrichment scores at each nucleotide position in a .wig file format
score_chr	Calculate read-enrichment scores for each nucleotide position
sigWin	Calculate regions of read-enrichment
sigWin_chr	Calculate regions of read-enrichment
TAIR8_genes_test	Partial dataset of a ChIP-seq experiment