merging_libraries {BgeeCall} | R Documentation |
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.
merging_libraries( userFile = NULL, approach = "BH", condition = "species_id", cutoff = 0.05, outDir = NULL )
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 |
A dataframe containing the minimum quantitative value (p-value or q-value) and the calls to each gene id for the referent condition.
Sara Fonseca Costa
## 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)