normWrapper {SCnorm} | R Documentation |
This function iteratively normalizes using K groups and then evaluates whether K is sufficient. If the maximum mode received from the GetK() function is larger than .1, K is increased to K + 1. Uses params sent from SCnorm.
normWrapper( Data, SeqDepth = NULL, Slopes = NULL, CondNum = NULL, PrintProgressPlots, PropToUse, Tau, Thresh, ditherCounts )
Data |
can be a matrix of single-cell expression with cells
where rows are genes and columns are samples. Gene names should
not be a column in this matrix, but should be assigned to rownames(Data).
Data can also be an object of class |
SeqDepth |
sequencing depth for each cell/sample. |
Slopes |
per gene estimates of the count-depth relationship. |
CondNum |
name of group being normalized, just for printing messages. |
PrintProgressPlots |
whether to automatically produce plot as SCnorm determines the optimal number of groups (default is FALSE, highly suggest using TRUE). Plots will be printed to the current device. |
PropToUse |
proportion of genes closest to the slope mode used for the group fitting, default is set at .25. This number #' mainly affects speed. |
Tau |
value of quantile for the quantile regression used to estimate gene-specific slopes (default is median, Tau = .5 ). |
Thresh |
threshold to use in evaluating the sufficiency of K, default is .1. |
ditherCounts |
whether to dither/jitter the counts, may be used for data with many ties, default is FALSE. |
matrix of normalized and scaled expression values for all conditions and the evaluation plots are output for each attempted value of K.
Rhonda Bacher