mappabilityCalc: Calculate The Mappability of a Region

Description Usage Arguments Details Value Author(s) Examples

Description

Function to calculate mappability of windows

Usage

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  ## S4 method for signature 'GRanges,MappabilitySource'
mappabilityCalc(x, organism, window = NULL,
              type = c("block", "TSS", "center"), verbose = TRUE)
  ## S4 method for signature 'data.frame,MappabilitySource'
mappabilityCalc(x, organism, window = NULL,
                                         type = c("block", "TSS", "center"), ...)

Arguments

x

A GRanges object or a data.frame, with columns chr and either position or start, end and strand.

window

Bases around the locations that are in the window. Calculation will consider windowSize/2 bases upstream, and windowSize/2-1 bases downstream.

For unstranded features, the effect is the same as for + strand features.

type

What part of the interval to make the window around. If the value is "TSS", the the start coordinate is used for all + strand features, and the end coordinate is used for all - strand features. If "cemter" is chosen, then the coordinate that is half way between the start and end of each feature will be used as the reference point. "block" results in the use the start and end coordinates without modification.

organism

The BSgenome object to calculate mappability upon, or the file path to a FASTA file generated by GEM Mappability, or the path to a bigWig file containing mappability scores.

verbose

Whether to print the progess of processing.

...

The verbose variable for the data.frame method, passed onto the GRanges method.

Details

The windows considered will be windowSize/2 bases upstream and windowSize/2-1 bases downstream of the given position of stranded features, and the same number of bases towards the start and end of the chromosome for unstranded features. The value returned for each region is a percentage of bases in that region that are not N (any base in IUPAC nomenclature).

For any positions of a window that are off the end of a chromosome, they will be considered as being N.

Value

A vector of mappability percentages, one for each region.

Author(s)

Aaron Statham

Examples

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  ## Not run: 
    require(BSgenome.Hsapiens36bp.UCSC.hg18mappability)
    TSSTable <- data.frame(chr = paste("chr", c(1,2), sep = ""), position = c(100000, 200000))
    mappabilityCalc(TSSTable, Hsapiens36bp, window = 200, type = "TSS")
  
## End(Not run)

Repitools documentation built on Nov. 17, 2017, 12:46 p.m.