filter.genes {metaseqR} | R Documentation |
This function performs the gene expression filtering
based on gene read counts and a set of gene filter rules.
For more details see the main help pages of
metaseqr
.
filter.genes(gene.counts, gene.data, gene.filters, sample.list)
gene.counts |
a matrix of gene counts, preferably after the normalization procedure. |
gene.data |
an annotation data frame usually
obtained with |
gene.filters |
a named list with gene filters and
their parameters. See the main help page of
|
sample.list |
the list containing condition names and the samples under each condition. |
a named list with three members. The first member
(result
is a named list whose names are the
gene filter names and its members are the filtered
rownames of gene.data
. The second member
(cutoff
is a named list whose names are the
gene filter names and its members are the cutoff
values corresponding to each filter. The third member
is a matrix of binary flags (0 for non-filtered, 1
for filtered) for each gene. The rownames of the
flag matrix correspond to gene ids.
Panagiotis Moulos
data("mm9.gene.data",package="metaseqR") gene.counts <- mm9.gene.counts sample.list <- sample.list.mm9 gene.counts <- normalize.edger(as.matrix(gene.counts[,9:12]), sample.list) gene.data <- get.annotation("mm9","gene") gene.filters <- get.defaults("gene.filter","mm9") filter.results <- filter.genes(gene.counts,gene.data, gene.filters,sample.list)