merging_libraries {BgeeCall} | R Documentation

## 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)

[Package BgeeCall version 1.8.0 Index]