addMaxEnt: addMaxEnt: Extract subset of data contained in given range...

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

addMaxEnt adds new columns to object data which contain MaxEnt-Score derived values. mxe_ps5 contains score5 values for left align-gap (exon-intron) boundary (i.e. assumed to reside on '+'-strand. mxe_ps3 contains score3 (maxent) values for right align-gap (intron-exon) boundary (i.e. assumed to reside on '+'-strand). mxe_ms5 contains score5 values for right align-gap (exon-intron) boundary on reverseComplement transformed sequence (i.e. assumed to reside on '-'-strand). mxe_ms3 contains score3 values for left align-gap (intron-exon) boundary on reverseComplement transformed sequence (i.e. assumed to reside on '-'-strand). From these values, s3strand, s5strand and meStrand are derived: s3strand is '+' when mxe_ps5 >= mxe_ms5 and '-' otherwise; s3strand is '+' when mxe_ps3 >= mxe_ms3 and '-' otherwise. meStrand equals s5strand when s5strand=s3strand and '*' otherwise. The function setMeStrand copies existing meStrand values into strand column (and throws an error when meStrand does not exist).

Usage

addMaxEnt(x,dna,maxent,digits=1)

Arguments

x

gapSites.

dna	DNAStringSet. Reference sequence identifier.

maxent

maxEnt. Contains score table which are internally used by score3 and score5 methods.

digits

Numeric. Default value: 1. Internally calculated maxent scores are rounded to given number of decimal places.

Value

gapSites

Author(s)

Wolfgang Kaisers

Examples

# A) Read gapSites
bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
bamClose(reader)

# B) Load DNA
dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
load(dnafile)

# C) maxEnt
mes<-load.maxEnt()
gae<-addMaxEnt(ga,dna_small,mes)
getMeStrand(gae)
sae<-setMeStrand(gae)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.