Description Usage Arguments Details Examples
Filter out genes that are not suitable for differential expression analysis.
1 | filter_gene(dfname, minmean = 2, n0prop = 0.2, minsd = 1)
|
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 |
This function filter.genes
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
.
1 2 | dat <- matrix(rnbinom(300*60, mu = 2, size = 1), 300, 60)
dat_filtered <- filter_gene(dat, minmean=2, n0prop=0.2, minsd=1)
|
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