Nucleosome Free Regions (NFR) score

NFR score is a raio between cut signal adjacent to TSS and that flanking the corresponding TSS. Each TSS window of 400 bp is first seperated into 3 sub-regions: the most upstream 150 bp (n1), the most downstream of 150 bp (n2), and the middle 100 bp (nf). Then the number of fragments with 5' ends overlapping each region are calculated for each TSS. The NFR score for each TSS is calculated as NFR-score = log2(nf) - log2((n1+n2)/2). A plot can be generate with the NFR scores as Y-axis and the average signals of 400 bp window as X-axis, very like a MA plot for gene expression data.

NFRscore(
  obj,
  txs,
  seqlev = intersect(seqlevels(obj), seqlevels(txs)),
  nucleosomeSize = 150,
  nucleosomeFreeSize = 100
)

Arguments

obj	an object of GAlignments
txs	GRanges of transcripts
seqlev	A vector of characters indicates the sequence levels.
nucleosomeSize	numeric(1) or integer(1). Default is 150
nucleosomeFreeSize	numeric(1) or integer(1). Default is 100

Value

A object of GRanges with NFR scores

Author

Jianhong Ou

Examples

 
library(GenomicRanges)
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
bamfile <- system.file("extdata", "GL1.bam", 
                       package="ATACseqQC", mustWork=TRUE)
gal1 <- readBamFile(bamFile=bamfile, tag=character(0), 
                    which=GRanges("chr1", IRanges(1, 1e6)), 
                    asMates=FALSE)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#> Loading required package: GenomicFeatures
#> Loading required package: AnnotationDbi
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
txs <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
nfr <- NFRscore(gal1, txs)