aaGapSites-class: Class '"aaGapSites"'

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

Description

Contains gapAligns data and a AAStringSet.

Objects from the Class

Objects can be created by calls of the form new("aaGapSites", ...).

Slots

seq:

"AAStringSet": Contains amino acid sequences.

nAligns:

"numeric": Contains total number of aligns.

nAlignGaps:

"numeric": Contains total number of align gaps.

dt:

"data.frame": Contains data for all gap sites.

Extends

Class "gapSites", directly.

Methods

head

signature(x = "aaGapSites"): Returns the first lines of object.

show

signature(object = "aaGapSites"): Returns the last lines of object.

truncateSeq

signature(x="caRanges",rme=TRUE,trunc=42L): Truncates contained sequence when character (given by ASCII code in trunc). The default (42L) encodes for character '*' which indicates stop-codon.

trypsinCleave

signature(x = "caRanges",minLen = 5): Performs in silico trypsinization of contained sequence. The sequence fragment which contains the (position depicted) exon-intron boundary is returned. Datasets for which the truncated sequence is shorter than minLen are excluded.

write.files

signature(x = "caRanges"): Exports contained data into "csv" file.

Author(s)

Wolfgang Kaisers

Examples

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

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

# C) Calculate cross junctional ranges
lrj <- lrJunc(ga, lfeatlen=6, rfeatlen=6, strand='+')
lr1 <- lrCodons(lrj, frame=1, strand='+')
lr2 <- lrCodons(lrj, frame=2, strand='+')
lr3 <- lrCodons(lrj, frame=3, strand='+')
lr <- c(lr1, lr2, lr3)

# D) Add DNA-sequence
lrd <- dnaGapSites(lr, dna_small)

# E) Translate DNA to amino acid
lra <- translate(lrd)

spliceSites documentation built on May 6, 2019, 3:05 a.m.