create_dataset: Generating the dataset for the meta-analysis

In Ilarius/metaDEA: Perform co-DE gene analysis

Generating the dataset for the meta-analysis

Description

Given a number of differential expression analyses it creates a dataset with the right format for the downstream analyses.

Usage

create_dataset(
  ...,
  col_names = "GeneName",
  col_adjpvals = c("adj.P.Val", "padj"),
  col_log2FC = c("logFC", "log2FoldChange")
)

Arguments

...	dataframes with the differential expression analyses to be included in the final dataset.
col_names	character vector with all the possible column names that indicate the gene names in the input dataframes. If this column is absent the rownames will be used as gene names.
col_adjpvals	character vector with all the possible column names that indicate the adjusted p-value in the input dataframes.
col_log2FC	character vector with all the possible column names that indicate the log2 fold changes in the input dataframes.

Value

dataset list of lists, including a list called names containing sublists, each corresponding to a specific comparison from a study, of differentially expressed genes (each sublist is a character vector). The sublists are named with the names given to each of the objects given as differential expression analyses.

Examples

# import dataset with DESeq2 differential expression analysis
data("ipsc_deseq2")
# import dataset with limma differential expression analysis
data("thymus_limma")
list_array_2studies=create_dataset(thymus_limma, ipsc_deseq2,col_names="GeneName", col_adjpvals=c("adj.P.Val", "padj"), col_log2FC=c("logFC", "log2FoldChange"))

Ilarius/metaDEA documentation built on May 6, 2023, 6:47 p.m.