R: Class '"exonAlignDepth"': Align-depth data for single genes...

exonAlignDepth-class {rbamtools} | R Documentation

## Class `"exonAlignDepth"`: Align-depth data for single genes on multiple samples (BAM files). Intronic regions are cut out of align depth matrix.

### Description

Objects of this class combine data from `geneAlignDepth`. During construction, the align depth matrix is segmentized, so that only (unified) exonic regions are represented in align depth matrix.

### Objects from the Class

Objects can be created by calls of the form `exonAlignDepth(sal)`.

### Slots

ald

  `"matrix"`: Matrix containing alignment depth data.

aldRatio

  `"data.frame"`: Contains mean alignment depth and alignment-depth-ratio data. `nr` is the ratio between the in-place and next alignment depth. `pr` is the ratio between in-place and previous alignment depth.

junctions

  `"data.frame"`: Contains alignment-gap-sites which had been generated when reading `geneAlignDepth` data.

`gene_id`:

  `"character"`: Gene identifier (e.g. Ensembl or UCSC).

`gene_name`:

  `"character"`: Gene name.

`seq_name`:

  `"character"`: Reference sequence (chromosome) name.

`strand`:

  `"character"`: Strand orientation of gene on reference sequence (+, - or *)

`nAligns`:

  `"numeric"`: Total number of alignments in each BAM file.

`group`:

  `"factor"`: Group assignment

label

  `"character"`: Short textual identifier for each sample.

### Methods

show

  `signature(object="exonAlignDepth")`: Prints a short message with some summarizing data.

exonAlignDepth

  `signature(object=c("sampleBamFiles", "geneModel"`: Constructs `exonAlignDepth` object and reads align depth data from BAM files.

plot

  `signature(object="exonAlignDepth")`: Plots align depth data.

aldRatio

  `signature(object="exonAlignDepth")`: Returns data.frame containing alignment-depth-ratio data used for identification of exon junctions.

junctionSites

  `signature(object="exonAlignDepth")`: Returns data.frame containing junction positions.

getNormFactor

  `signature(object="exonAlignDepth")`: Returns numeric value which will be uses for plotting and `groupAldMatrix` and `groupAldTable`.

groupAldMatrix

  `signature(object="exonAlignDepth")`: Returns matrix containing mean alignment depth values. Data for each sample is stored in one column. Data for each genomic position is stored in one row. A summarizing function `f` may be given (Default is `mean`).

groupAldTable

  `signature(object="exonAlignDepth")`: Returns data.frame containing three columns. The first column contains genomic positions, the second position contains group assignment and the third position contains (normalized) alignment dept values. A summarizing function `f` may be given (Default is `mean`).

### Author(s)

Wolfgang Kaisers

### Examples

    ## - - - - - - - - - - - - - - - - - - - - - - ##
    # Construct sampleBamFiles object
    bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
    bs <-sampleBamFiles(1)
    bamFiles(bs) <- bam
    sampleLabels(bs) <- "s1"
    sampleGroups(bs) <- "g1"
    checkBamFiles(bs)
    nAligns(bs) <- bamCountAll(bs)
    bs
    ## - - - - - - - - - - - - - - - - - - - - - - ##
    # Construct geneModel object
    library(refGenome)
    ucfile<-system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
    uc<-loadGenome(ucfile)
    gt <- getGeneTable(uc)
    gene_id <- as.character(gt$gene_id[1])
    gm <- geneModel(uc, gene_id)
    ## - - - - - - - - - - - - - - - - - - - - - - ##
    # Construct geneAlignDepth object
    gad <- geneAlignDepth(bs, gm)
    ## - - - - - - - - - - - - - - - - - - - - - - ##
    # Extract exonAlignDepth object
    ead <- exonAlignDepth(gad, ratioLim=5, infVal=1000)
    ald <- aldRatio(ead)
    jc <- junctionSites(ead)
    getNormFactor(ead)
    cead <- cutFlatAlignDepth(ead, ratio=0.1)

[Package rbamtools version 2.16.17 Index]