aaGapSites-class {spliceSites} | R Documentation

## Class `"aaGapSites"`

### 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)

[Package spliceSites version 1.31.0 Index]