seqbias (version 1.20.0)

seqbias.predict: Predicting sequencing bias

Description

Predicts sequencing bias given a fit seqbias model

Usage

seqbias.predict(sb, I)

Arguments

sb

a seqbias object

I

a GRanges object

Value

A list of numeric vectors are returned, one for each genomic interval in I. The vectors are of equal length to the interval given, and the predicted sequencing bias is given for each position.

Details

Once a seqbias model is fit with 'seqbias.fit', the sequencing bias of any region in the reference sequence can be predicted using this function. Given the coordinates of a region, this function produces a vector of the same length as the sequence. Each position 'i' is given a sequence score 'v_i'.

A simple procedure is then to normalize read counts given the sequencing bias. The read count of (i.e. the number of reads beginning on) position 'i', denoted by 'x_i', can be normalized by computing 'x_i/v_i', giving an estimate of abundance that is more accurate in expectation.

See Also

seqbias.fit

Examples

  reads_fn <- system.file( "extra/example.bam", package = "seqbias" )
  ref_fn <- system.file( "extra/example.fa", package = "seqbias" )

  sb <- seqbias.fit( ref_fn, reads_fn )

  I <- GRanges( c('seq1'), IRanges( c(1), c(5000) ), strand = c('-') )

  bias <- seqbias.predict( sb, I )