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)
either a data frame or the name of a tab-separated file from which copy number data can be read. The rows of the data frame or file should represent the probes. Column 1 must hold numeric or character chromosome numbers, column 2 the numeric local probe positions, and subsequent column(s) the numeric copy number measurements for one or more samples. The header of copy number columns should give sample IDs.
the unit used to represent the probe positions. Allowed options are "mbp" (mega base pairs), "kbp" (kilo base pairs) or "bp" (base pairs). By default assumed to be "bp".
optional character vector containing chromosome arms (denoted 'p' and 'q') corresponding to the chromosomes and positions found in
data. If not specified chromosome arms are found using the built-in genome assembly version determined by
either a data frame or the name of a tab-separated file containing original copy number data in the case where
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
minimum number of probes in each segment, default is 5.
penalty for each discontinuity in the curve, default is 40.
logical value indicating whether the copy number measurements should be scaled by the sample residual standard error. Default is TRUE.
a logical value indicating whether a fast (not guaranteed to be exact) version should be run on chromosome arms with > 400 probes.
a string specifying which genome assembly version should be applied to determine chromosome arms. Allowed options are "hg19", "hg18", "hg17" and "hg16" (corresponding to the four latest human genome annotations in the UCSC genome browser).
the number of decimals to be applied when reporting results. Default is 4.
logical value indicating whether a data frame holding copy number estimates (pcf values) should be returned along with the segments. Default is FALSE, which means that only segments are returned.
logical value indicating whether results should be saved in text files.
optional character vector of length two giving the name of the files where the pcf estimates and segments, respectively, should be saved in case
logical value indicating whether or not to print a progress message each time pcf analysis is finished for a new chromosome arm.