R: Class '"GenomePartition"': .

GenomePartition-class {rbamtools} | R Documentation

## Class `"GenomePartition"`: .

### Description

.

### Details

The environment contains at least three objects: `reftable`, `reflist` and `genome`. The reftable data.frame contains data on reference sequences (chromosomes) derived from the bamReader `getRefData` function. The reflist is a list containing calculated partition segments based on the `genome` argument of the genomePartition function and a underlying equidistant grid on the genome. After counting BAM alignments using a genomePartition object, the environment additionally contains a filetable data.frame.

### Objects from the Class

can be created using the `genomePartition` function on an opened bamReader and a data.frame containing target regions (usually gene annotation data).

### Slots

`ev`:

  `"environment"`. Environment which contains data as data.frames.

### Methods

show

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

getSeqNr

  `signature(object="GenomePartition")`: Returns number of reference sequences in refdata.

getRefData

  `signature(object="GenomePartition")`: Returns refdata data.frame.

getPos

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

countPartition

  `signature(partition="GenomePartition", src="bamReader")`: Counts BAM alignments on the contained grid from a single BAM file (represented by an opened bamReader.

countPartition

  `signature(partition="GenomePartition", src="data.frame")`: Counts BAM alignments on the contained grid from multiple BAM files (filenames and sample names given in src)

checkPartition

  `signature(partition="GenomePartition", src="data.frame", verbose="logical")`: Checks incoming arguments and present reference sequences for consistency. Intended to be used as preparation for `countPartition` in order to prevent unexpected routine terminations.

getFileTable

  `signature(object="GenomePartition")`: Returns the contained filetable (constituted by usage of `countPartition` function).

getAlignCounts

  `signature(object="GenomePartition")`: Returns counted alignments in annotated regions (exons, genes).

getGridAlignCounts

  `signature(object="GenomePartition")`: Returns counted alignments in underlying equidistant grid.

### Author(s)

Wolfgang Kaisers

### Examples

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

    # Provide exon positions
    id <- 1:13
    seqid <- "chr1"
    gene <- "WASH7P"
    ensg_id <- "ENSG00000227232"
    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)

    ref <- data.frame(id=id, seqid=seqid, begin=start, end=end, gene=gene, ensg=ensg_id)

    # Create partition (adds equidistant grid)
    partition <- genomePartition(reader, ref)

    # Count alignments
    countPartition(partition, reader)

    # Extract result data
    urc <- getAlignCounts(partition)
    gac <- getGridAlignCounts(partition)

[Package rbamtools version 2.16.17 Index]