ORAfilename <- function(OutFile, NrOfValidInputGenes, Correction, PvalueThreshold, MinNrOfGenes, OnlyManuCur,# ABCAnalysis, ImpThreshold
WithRefSet = FALSE){
# Function to complete the OutFile name passed to dbtORA with ORA parameters.
# OutFilePlusParams <- ORAfilename(OutFile, NrOfValidInputGenes, Correction, PvalueThreshold, MinNrOfGenes, OnlyManuCur)
# # # OutFilePlusParams <- ORAfilename(OutFile, NrOfValidInputGenes, Correction, PvalueThreshold, MinNrOfGenes, OnlyManuCur, ABCAnalysis, ImpThreshold)
# INPUT:
# Most of the parameters given to dbtORA (default values set in dbtORA!):
# OutFile String;
# Filename of the output file(s). Will be complemented by the parameters of the ORA.
# NrOfValidInputGenes String;
# Number of valid input genes = #(input genes) - #(duplicated and non-annotated genes)
# Correction String;
# Type of correction for mulitple testing of the p-values.
# 'BON' for Bonferroni,
# 'FDR' for False Discovery Rate,
# 'RAW' if no correction should be done.
# PvalueThreshold Numeric;
# P-value threshold. GO-Terms with p-values greater than PvalueThreshold will be ignored.
# MinNrOfGenes Numeric;
# Minimum number of genes annotated to one Term that is accepted. GO-Terms with more than
# MinNrOfGenes genes will be considered in calculation.
# OnlyManuCur Boolean;
# Set TRUE if only manually curated gene annotations should be considered.
# # # ABCAnalysis Boolean;
# # # Do an ABC analysis to curt the vector of GO terms used to draw the DAG to group A terms.
# # # ImpThreshold Numeric;
# # # Importance Threshold. If the calculated importance of a term is smaller than ImpThreshold,
# # # the term won't occur in the DAG.
# WithRefSet Boolean;
# Set TRUE if RefSet given. Default: FALSE.
# OUTPUT:
# OutFilePlusParams String;
# The complemented OutFile without ext.
# AUTHOR:
# CL, 03.03.2016
# USES:
# [1] "function" "require" "basename" "file_path_sans_ext"
# [5] "paste0" "paste" "if" "return"
# requireNamespace('tools')
# requireNamespace('utils')
# Wir muessen die Dateiendung entfernen, sofern gegeben, und Parameter anfuegen.
# Punkte im Dateinamen zulassen, falls es nicht die Punkte vor den folgenden Endungen sind:
if(tools::file_ext(OutFile)%in% c('pdf', 'png', 'names', 'lrn', 'eps', 'txt')){
OutFileWithoutExt <- basename(tools::file_path_sans_ext(OutFile))
}else{
OutFileWithoutExt <- OutFile
}
OutFileWithoutExt <- paste0(OutFileWithoutExt, 'Genes', NrOfValidInputGenes)
OutFilePlusParams <- paste(OutFileWithoutExt, Correction, PvalueThreshold, MinNrOfGenes, sep='_')
if(OnlyManuCur){
OutFilePlusParams <- paste(OutFilePlusParams, 'MANU', sep = '_')
}else{
OutFilePlusParams <- paste(OutFilePlusParams, 'ALL', sep = '_')
}# end if(OnlyManuCur)
# if(ABCAnalysis){
# OutFilePlusParams <- paste(OutFilePlusParams, 'ABC', sep = '_')
# }
# if(ImpThreshold != 0){
# OutFilePlusParams <- paste(OutFilePlusParams, 'ImpThresh', sep = '_'
# }
if(WithRefSet){
OutFilePlusParams <- paste(OutFilePlusParams, 'RefSet', sep= '_')
}
return(OutFilePlusParams)
}# end function ORAfilename
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