getSlopes {SCnorm} | R Documentation |
This is the gene-specific fitting function, where a median (Tau = .5) quantile regression is fit for each gene. Only genes having at least 10 non-zero expression values are considered.
getSlopes(Data, SeqDepth = 0, Tau = 0.5, FilterCellNum = 10, ditherCounts = FALSE)
Data |
matrix of un-normalized expression counts. Rows are genes and columns are samples. |
SeqDepth |
vector of sequencing depths estimated as columns sums of un-normalized expression matrix. |
Tau |
value of quantile for the quantile regression used to estimate gene-specific slopes (default is median, Tau = .5 ). |
FilterCellNum |
the number of non-zero expression estimate required to include the genes into the SCnorm fitting (default = 10). The initial |
ditherCounts |
whether to dither/jitter the counts, may be used for data with many ties, default is FALSE. |
vector of estimated slopes.
Rhonda Bacher
data(ExampleSimSCData) myslopes <- getSlopes(ExampleSimSCData)