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Convert a data frame to a tmod object
makeTmodFromDataFrame.Rd
Convert a data frame to a tmod object
Usage
makeTmodFromDataFrame(
df,
feature_col = 1,
module_col = 2,
title_col = NULL,
extra_module_cols = NULL,
extra_gene_cols = NULL
)
Arguments
- df
A data frame
- feature_col
Which column contains the feature (gene) IDs
- module_col
Which column contains the module (gene set) IDs
- title_col
Description of the modules (if NULL, the description will be taken from the module_col)
- extra_module_cols
Additional columns to include in the module data frame
- extra_gene_cols
Additional gene columns to include in the genes data frame
Details
`makeTmodFromFeatureDataFrame` converts mapping information from features (genes) to modules (gene sets). The data frame has a row for each feature-module pair.
`makeTmodFromModuleDataFrame` converts mapping information from features (genes) to modules (gene sets). The data frame has a row for each module, and all gene IDs corresponding to a module are stored as a comma separated string, e.g.
Vice versa, `tmod2DataFrame` converts a tmod object to a data frame.
Examples
df <- data.frame(
gene_id=LETTERS[1:10],
geneset_id=rep(letters[1:2], each=5),
geneset_description=rep(paste0("Gene set ", letters[1:2]), each=5))
res <- makeTmodFromDataFrame(df,
feature_col="gene_id",
module_col="geneset_id",
title_col="geneset_description")
#> making Tmod