R: Class '"alignDepth"': Alignment depth information from...

alignDepth-class {rbamtools} | R Documentation

## Class `"alignDepth"`: Alignment depth information from bamRange objects.

### Description

The alignDepth class represents data and provides plot functions for alignment depth for genomic regions (represented by bamRange objects).

### Details

The `params` vector contains the following values:

1 | seqid | 0-based index of reference sequence
2 | qrBegin | 0-based left boundary of query region (query range begin)
3 | qrEnd | 0-based right boundary of query region (query range end)
4 | complex | 0= all aligns included, 1= only aligns with n_cigar > 1 included
5 | rSeqLen | Length of reference sequence
6 | qSeqMinLen | Minimum of query sequence length (= read length)
7 | qSeqMaxLen | Maximum of query sequence length (= read length)

### Objects from the Class

Objects can be created by calls of the form `alignDepth(object,gap))` on bamRange objects. From the `bamRange` object, the range is extracted and for each nucleotide position whithin this range the numbers of align matches are calculated. When `alignDepth` is called wich `gap=TRUE`, the function counts aligns solely for gap-adjacent match regions (cigar-op's).

### Slots

`depth`:

  `"integer"`. Align depth values.

`pos`:

  `"integer"`. Corresponding (1-based) positions

`params`:

  `"numeric"`. Set of internally used parameters

`refname`:

  `"character"`. Name of reference sequence from which `bamRange` was extracted.

### Methods

show

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

plotAlignDepth

  `signature(object="alignDepth", main, xlab, ylab, start, end, transcript, xlim, strand,"...")`: Plots align depth in a line-plot.

getDepth

  `signature(object="alignDepth")`: Returns numeric align depth values.

getPos

  `signature(object="alignDepth")`: Returns numeric position values for align depth.

getParams

  `signature(object="alignDepth")`: Returns numeric parameter values.

### Author(s)

Wolfgang Kaisers

### Examples

    # Open (indexed) BAM file
    bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
    reader<-bamReader(bam,idx=TRUE)

    # Extract reads from BAM file
    xlim = c(10000, 30000)
    coords<-c(0,xlim[1], xlim[2])
    range<-bamRange(reader,coords)
    bamClose(reader)

    # Calculate align depth
    ad<-alignDepth(range)
    ad
    getParams(ad)

    # Prepare plotting parameter
    gene<-"WASH7P"
    ensg_id <- "ENSG00000227232"
    enst_id <- "ENST00000538476"

    # Get exon positions
    start<-c(14411,15000,15796,15904,16607,16748,16858,17233,17602,17915,18268,24737,29534)
    end <- c(14502,15038,15901,15947,16745,16765,17055,17364,17742,18061,18366,24891,29806)

    # Do plot
    plotAlignDepth(ad, lwd = 2, xlim = xlim,
                main = paste("Align depth for gene",gene),
                ylab = "Align depth", start = start,
                end = end, strand = "-",
                transcript = paste("Chromosome 1",
                "\tGene", ensg_id,
                "\tTranscript ",enst_id)
    )

[Package rbamtools version 2.16.17 Index]