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

exonLoessModel-class {rbamtools} | R Documentation

## Class `"exonLoessModel"`: 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 `exonLoessModel(sal)`.

### Slots

`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`:

  `"character"`: Group assignment

`loessPred`:

  `"matrix"`: Loess estimated align depth values for each group. Each column contains estimates for one group.

### Methods

show

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

exonLoessModel

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

plot

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

groupRatio

  `signature(object="exonLoessModel", lim="numeric")`: Returns single numeric value. From align depth estimates in loessPred matrix, the ratio between a column and the precedent column is calculated. For each position, the minimum ratio is extracted. The function returns the relative number of positions, where the minimum ratio exceeds given `lim` value.

### 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 exonLoessModel object
    ead <- exonAlignDepth(gad, ratioLim=5, infVal=1000)
    elm <- exonLoessModel(ead)
    celm <- cutFlatAlignDepth(elm, ratio=0.1)
    groupRatio(celm, lim=1.2, cut=0, order=1)

[Package rbamtools version 2.16.17 Index]