fractionAltered {snapCGH} | R Documentation |
Function to compute fraction of genome altered for each sample
Description
This function outputs lists containing proportions of the genome that
are gained and lost for each sample.
Usage
fractionAltered(input, thres = 0.25, factor = 2.5,
samplenames = colnames(input$M),
chrominfo = chrominfo.Mb)
Arguments
input |
An object of type MAList or SegList |
thres |
either a vector providing unique threshold for
each sample or a vector of the same length as number of
samples providing sample-specific
threshold. Clone is considered to be gained if
it is above the threshold and lost if it is below negative
threshold. Defaults to 0.25 |
factor |
specifies the number by which experimental
variability should be multiples. Used only when tumor
specific variability in 'input' is not NULL or when factor is greater than 0. Defaults to
2.5. |
samplenames |
Sample names. Default is the column names of the
aCGHList object |
chrominfo |
A chromosomal information associated with the mapping of the
data. Default is chrominfo.Mb |
Value
gainP |
Vector of proportion of genome gained for each sample |
lossP |
Vector of proportion of genome lost for each sample |
Author(s)
Jane Fridlyand, Ritu Roydasgupta
[Package
snapCGH version 1.0.0
Index]