merging_libraries: Calls of expression in combined libraries

In BgeeDB/BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

Calls of expression in combined libraries

Description

Merging/combine libraries based in a condition specified by the user. The merging can be done using the p-values of the libraries, by applying the BH method, or using the q-values of the libraries using the fdr_inverse method.

Usage

merging_libraries(
  userFile = NULL,
  approach = "BH",
  condition = "species_id",
  cutoff = 0.05,
  outDir = NULL
)

Arguments

userFile	A file provided by the user with correspondent conditions
approach	Approach used to do the merging of libraries
condition	Condition/s where the merging should be done
cutoff	Cutoff that should be applied to call Present/Absent genes
outDir	Directory where the output files should be saved

Value

A dataframe containing the minimum quantitative value (p-value or q-value) and the calls to each gene id for the referent condition.

Author(s)

Sara Fonseca Costa

Examples

## Not run: 
callsMerging_species <- merging_libraries(userFile = 'PATH_USER_FILE', approach = 'BH', 
condition = 'species_id', cutoff = 0.05, outDir = 'PATH_OUTPUT')
callsMerging_species_sex <- merging_libraries(userFile = 'PATH_USER_FILE', approach = 'fdr_inverse', 
condition = c(species_id, sex), cutoff = 0.01, outDir = 'PATH_OUTPUT')
callsMerging_all <- merging_libraries(userFile = 'PATH_USER_FILE', approach = 'fdr_inverse', 
condition = c(species_id, anatEntity, devStage, sex, strain), cutoff = 0.05, outDir = 'PATH_OUTPUT')

## End(Not run)

BgeeDB/BgeeCall documentation built on Nov. 10, 2023, 5:40 a.m.