A function checking if your de_container
contains everything you need
Source: R/mosdef_check_inputs.R
mosdef_de_container_check.Rd
A function checking if your de_container
contains everything you need
Arguments
- de_container
An object containing the data for a Differential Expression workflow (e.g.
DESeq2
,edgeR
orlimma
). Currently, this can be aDESeqDataSet
object, normally obtained after running your data through theDESeq2
framework.- verbose
Logical, whether to add messages telling the user which steps were taken.
Examples
library("macrophage")
library("DESeq2")
data(gse, package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
#> using counts and average transcript lengths from tximeta
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
keep <- rowSums(counts(dds_macrophage) >= 10) >= 6
dds_macrophage <- dds_macrophage[keep, ]
# dds_macrophage <- DESeq(dds_macrophage)
mosdef_de_container_check(dds_macrophage)