R: saveAldData: Save alignment depth plots for single genes

saveAldData {rbamtools} | R Documentation

## saveAldData: Save alignment depth plots for single genes

### Description

The function `saveAldData` reads alignment data for all genes in `geneList` sequentially from all Bam files listed in `sampleBamFiles`. The function cuts out intronic regions using the `exonAlignDepth` class and calculates a smoothed groupwise estimate using the `exonLoessModel` function. In a second region cutting step, remaining regions with low alignment depth are cut out using `cutFlatAlignDepth`. Finally, the function calculates group-wise ratios of alignment depth using the `groupRatio` function.

### Usage

    saveAldData(bs, gl, path, order=NULL, lim=1.1, startId=1, f=mean)

### Arguments

`bs` | sampleBamFiles. Contains BAM file names and group assignment.

`gl` | geneList. Contains a list of `geneModel` objects. Only gene-name, gene-id and global genetic region is used. Object construction can be abridged using `interior=FALSE`.

`path` | character. Base directory where output files are written to.

`order` | numeric. Defines order in which group-levels of `sampleBamFiles` object are used for `groupRatio`

`lim` | numeric. Limit used for `groupRatio` function. The percentage of genomic position where this limit is exceeded between all (ordered) group levels is given as gr (and cgr) value in `aldrat` table.

`startId` | numeric. Index used for first gene. Starting value for subsequent numbering of genes.

`f` | function. Function for calculation of group accumulates. Defaults to `mean`. Alternatively `median` may also be used.

### Author(s)

Wolfgang Kaisers

### See Also

bamReader

### Examples

    bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
    reader <- bamReader(bam, idx=TRUE)
    # Extract data for HLHL17 gene:
    seqid <- "chr1"
    start <- 895967
    end <- 901099
    gene_name <- "HLHL17" # (optional)
    ranges <- data.frame(seqid=seqid, start=start, end=end, gene_name=gene_name)
    saveAldData(reader, ranges=ranges, filename="new_file.bam", f=mean)

[Package rbamtools version 2.16.17 Index]