Usage
track.table(..., .name, .parameters, .organism, .assembly, .chromosomes,
.makeNames = FALSE, .orderCols = TRUE, warn = TRUE)
track.bam(bamPath, baiPath, addChr, quiet = FALSE, .name, .organism,
.assembly, .parameters, warn = TRUE)
track.genes(...)
track.bands(...)
track.exons(...)
track.CNV(...)
Arguments
.name
Single character value, to fill the name
field inherited from
.
warn
Single logical value, to be passed to the appropriate check
method. Other conversion warnings rely on this value too in track.table
.
.parameters
A list
of drawing parameters, to fill the parameters
field of the object.
.organism
Single character value, to fill the organism
field of the object.
.assembly
Single character value, to fill the assembly
field of the object.
.chromosomes
Single character value, levels to use for the 'chrom' column if conversion to factor is needed.
.makeNames
Single logical value, whether to compute the 'name' column with unique values or not. If TRUE
, any existing 'name' column will be replaced.
.orderCols
Single logical value, whether to reorder the columns for more consistency between tracks or not.
bamPath
Single character value, the file name and path to a BAM file (.bam) to build a track around.
baiPath
Single character value, the file name and path to the corresponding BAI file (.bai) to build a track around. If missing, a guess will be tried (adding '.bai' to bamPath
or remplacing '.bam' by '.bai').
addChr
Single logical value, whether to automatically add 'chr' ahead chromosome names when querying or not. If missing, a guess will be tried looking for chromosome names beginning by 'chr' in the BAM header declaration.
quiet
Single logical value, whether to throw diagnostic messages during BAI parsing or not.