track-constructors {Rgb} | R Documentation |
Produces track.table
-inheriting objects.
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 to be passed to the inherited constructor ( |
.name |
Single character value, to fill the |
warn |
Single logical value, to be passed to the appropriate |
.parameters |
A |
.organism |
Single character value, to fill the |
.assembly |
Single character value, to fill the |
.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 |
.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 |
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. |
track.table
and track.bam
inheriting objects.
Sylvain Mareschal
track.table-class
, track.bam-class
# track.table from a data.frame df <- data.frame( chrom=1, strand="+", start=1:5, end=2:6, name=letters[1:5], stringsAsFactors=FALSE ) track.table(df) # track.table from vectors track.table(chrom=1, strand="+", start=1:5, end=2:6, name=letters[1:5]) # track.bam track.bam(system.file("extdata/ATM.bam", package="Rgb"))