getIdeogramData {gmoviz} | R Documentation

## Import transgenic genome data from .bam or .fasta file

### Description

Read in the seqname, start & end from .bam or .fasta file and format correctly for plotting with gmoviz.

### Usage

    getIdeogramData(bam_file = NULL, fasta_file = NULL,
      fasta_folder = NULL, just_pattern = NULL, unwanted_chr = NULL,
      wanted_chr = NULL, add_chr = TRUE)

### Arguments

`bam_file, fasta_file, fasta_folder` | Location of either a .bam file, .fasta file or folder of .fasta files to read in. You only need to supply one of these file types; .bam files are recommended because it is much faster than using .fasta files. Also note that the filters `unwatedChr`, `wanted_chr` and `just_pattern` won't work with single .fasta files (only with .bam or .fasta folders).
`just_pattern` | If supplied, this pattern (regex) will be used to select the sequences to read in
`unwanted_chr` | If supplied, these sequences won't be read in
`wanted_chr` | If supplied, only these sequences will be read in
`add_chr` | If `TRUE`, 'chr' will be added to the start of sequence names with one or two characters (e.g. X will become chrX and 10 will become chr10 but plasmid will remain as-is)

### Value

A GRanges containing the ideogram data (sequence names, starts & ends).

### See Also

The `gmovizInitialise` and `featureDiagram` functions which can be used to plot this data.

### Examples

    ## the example .bam file
    path <- system.file('extdata', 'ex1.bam', package='Rsamtools')

    ## just starting with 'seq'
    getIdeogramData(bam_file=path, just_pattern='^seq')

    ## only seq1
    getIdeogramData(bam_file=path, wanted_chr='seq1')

    ## not seq2 (same as above)
    getIdeogramData(bam_file=path, unwanted_chr='seq2')

    ## you can mix and match any of the filters
    getIdeogramData(bam_file=path, unwanted_chr='seq2', just_pattern='^seq')

    ## the function also works to read in individual .fasta files, but please
    ## note that for now the filters won't work (so if you have multiple
    ## sequences in one .fasta file then they will all be read in)
    path <- system.file('extdata', 'someORF.fa', package='Biostrings')
    getIdeogramData(fasta_file=path)

    ## we can also read in selected .fasta files from a folder of .fasta files,
    ## based on the filters shown above for the .bam file
    path <- system.file('extdata', 'fastaFolder', package='gmoviz')
    getIdeogramData(fasta_folder=path)

[Package gmoviz version 1.0.1 Index]