chromosomesPosition {CNAnorm} | R Documentation |
chrs
returns/set the name of chromosomes/contigs
arms
retruns the name of the chromosome and arm. A data frame containing
ideogram information has to be provided. See ?hg19_hs_ideogr for an example
pos
returns/set the position of starting window. Be careful!
If you need to change data, it is better to change the input data and start over.
chrs(object) ## S4 method for signature 'CNAnorm' pos(object, show = "start") ## S4 method for signature 'CNAnorm' arms(object, banding_df)
object |
An object of Class |
show |
The position to show: 'start', 'end' |
banding_df |
A data frame with infromation about ideogram |
chrs
and arms
return a character vector, pos
returns a numeric vector
Stefano Berri <s.berri@leeds.ac.uk>
gcNorm
, CNAnorm-class
, hg19_hs_ideogr
data(LS041) data(hg19_hs_ideogr) CN <- dataFrame2object(LS041) dataFrameNames <- as.character(LS041$Chr) objectNames <- chrs(CN) armNames <- arms(CN, hg19_hs_ideogr) # check the names are, indeed, the same all(dataFrameNames == objectNames) # make shorter names, drop the first three letters ('chr') shortNames <- substr(chrs(CN),4,nchar(chrs(CN))) chrs(CN) <- shortNames # retrieve all new names unique(chrs(CN)) unique(armNames)