| filter_gene {ClussCluster} | R Documentation |
Gene Filter
Description
Filters out genes that are not suitable for differential expression analysis.
Usage
filter_gene(dfname, minmean = 2, n0prop = 0.2, minsd = 1)
Arguments
dfname |
name of the expression data frame |
minmean |
minimum mean expression for each gene |
n0prop |
minimum proportion of zero expression (count) for each gene |
minsd |
minimum standard deviation of expression for each gene |
Details
Takes an expression data frame that has been properly normalized but NOT centered. It returns a list with the slot dat.ft being the data set that satisfies the pre-set thresholds on minumum mean, standard deviation (sd), and proportion of zeros (n0prop) for each gene.
If the data has already been centered, one can still apply the filters of mean and sd but not n0prop.
Value
a list containing the data set with genes satisfying the thresholds, dat.ft, the name of dat.ft, and the indices of those kept genes, index.
Examples
dat <- matrix(rnbinom(300*60, mu = 2, size = 1), 300, 60)
dat_filtered <- filter_gene(dat, minmean=2, n0prop=0.2, minsd=1)