pcf(data, pos.unit = "bp", arms = NULL, Y = NULL, kmin = 5, gamma = 40,
normalize = TRUE, fast = TRUE, assembly = "hg19", digits = 4,
return.est = FALSE, save.res = FALSE, file.names = NULL, verbose = TRUE)
data
. If not specified chromosome arms are found using the built-in genome assembly version determined by assembly
.data
contains Winsorized values. If provided, these values are used to calculate the mean of each segment, otherwise the copy number values in data
are used. Y
must be on the same form as data
.save.res=TRUE
.return.est = TRUE
a list with the following components:return.est = FALSE
, only the data frame containing the segments is returned.
If save.res = TRUE
the results are also saved in text files with names as specified in file.names
. If file.names=NULL
, a folder named "pcf_results" is created in the working directory, and the pcf estimates and segments are saved in this directory in tab-separated files named estimates.txt and segments.txt, respectively.multipcf
#Load the lymphoma data set:
data(lymphoma)
#Take out a smaller subset of 3 samples (using subsetData):
sub.lymphoma <- subsetData(lymphoma,sample=1:3)
#First winsorize data to handle outliers:
wins.lymph <- winsorize(sub.lymphoma)
#Run pcf (using small gamma because of low-density data):
pcf.segments <- pcf(data=wins.lymph,gamma=12,Y=sub.lymphoma)
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