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

geneAlignDepth-class {rbamtools} | R Documentation

## Class `"geneAlignDepth"`: Align-depth data for single genes on multiple samples (BAM files).

### Description

Objects of this class combine data from `geneModel` and from `sampleBamFiles` objects allowing to read BAM alings for gene defined regions from multiple BAM files. `geneAlignDepth` object contain an Align depth matrix which can be visualized using a generic plot function.

### Objects from the Class

Objects can be created by calls of the form `getgeneAlignDepth(gesa, gm)` .

### Slots

`bamFiles`:

  `"character"`: Location of BAM files

`bamIdxFiles`:

  `"character"`: Location of BAM index files

`nAligns`:

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

`group`:

  `"factor"`: Group assignment

label

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

length

  `"integer"`: Vector length for bamFiles, bamIdxFiles, nAligns, group and label.

ald

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

gapSites

  `"data.frame"`: Align gap sites data from genetic region.

ev

  `"environment"`: Contains additional data (e.g. group table).

`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 *)

`coords`:

  `"numeric"`: Gene coordinates (i.e. start and end position).

### Methods

show

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

geneAlignDepth

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

plot

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

### 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)
    plot(gad, col="gray50")

[Package rbamtools version 2.16.17 Index]