Arguments
X
Matrix of positive real values, where
columns are interpreted as samples and rows as genomic regions. An entry is
the read count of a sample in the genomic region. Alternatively this can be
a GRanges object containing the read counts as values.
chr
Character vector that has as many elements as "X" has rows. The
vector assigns each genomic segment to a reference sequence (chromosome).
normType
Type of the normalization technique. Each samples'
read counts are scaled such that the total number of reads are comparable across
samples.
If this parameter is set to the value "mode",
the read counts are scaled such that each samples'
most frequent value (the "mode") is equal after normalization.
Accordingly for the other options are "mean","median","poisson", "quant", and "mode".
Default = "poisson".
sizeFactor
By this parameter one can decide to how the size factors
are calculated.
Possible choices are the the mean, median or mode coverage ("mean", "median", "mode") or any quantile
("quant").
qu
Quantile of the normType if normType is set to "quant" .Real value between 0 and 1. Default = 0.25.
quSizeFactor
Quantile of the sizeFactor if sizeFactor is set to "quant".
0.75 corresponds to "upper quartile normalization". Real value between 0 and 1. Default = 0.75.
ploidy
An integer value for each sample or each column in the read
count matrix. At least two samples must have a ploidy of 2. Default = "missing".