filter.exons {metaseqR} | R Documentation |
This function performs the gene expression filtering
based on exon read counts and a set of exon filter rules.
For more details see the main help pages of
metaseqr
.
filter.exons(the.counts, gene.data, sample.list, exon.filters, restrict.cores = 0.8)
the.counts |
a named list created with the
|
gene.data |
an annotation data frame usually
obtained with |
sample.list |
the list containing condition names and the samples under each condition. |
exon.filters |
a named list with exon filters and
their parameters. See the main help page of
|
restrict.cores |
in case of parallel execution of
several subfunctions, the fraction of the available cores
to use. In some cases if all available cores are used
( |
a named list with two members. The first member
(result
is a named list whose names are the
exon filter names and its members are the filtered
rownames of gene.data
. The second 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("hg19.exon.data",package="metaseqR") exon.counts <- hg19.exon.counts gene.data <- get.annotation("hg19","gene") sample.list <- sample.list.hg19 exon.filters <- get.defaults("exon.filter") the.counts <- construct.gene.model(exon.counts,sample.list, gene.data) filter.results <- filter.exons(the.counts,gene.data, sample.list,exon.filters)