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dont_check_names used for data.frame and data.table evidence_file #152

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dont_check_names used for data.frame and data.table evidence_file #152

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fa15847
dont_check_names used for data.frame and data.table evidence_file
bpolacco Apr 9, 2020
0d78686
fix dont_check_names default and docstring; add a dropped x <-
bpolacco Apr 9, 2020
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22 changes: 8 additions & 14 deletions R/checkIfFile.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4,35 +4,29 @@
# either a path to a data file or a data object in data.frame or data.table
# form.
# @param input_file (object or data.frame) The filepath/object to be checked.
# @param dont_check_names if TRUE (default) names are not checked, otherwise
# names will be checked
# @param dont_check_names if TRUE names are not checked, otherwise
# names will be checked (default)
# @param is.evidence (logical) Whether or not the file to be read in is an
# evidence file. This will assign proper classes to the evidence file
# when being read in.
# @return An R data object
# @keywords internal, file, evidence, input
.artms_checkIfFile <- function(input_file,
dont_check_names = TRUE,
dont_check_names = FALSE,
is.evidence = FALSE) {
# check if already a data.frame or data.table
if (is.data.table(input_file)) {
x <- data.table(input_file)
x <- data.table(input_file, check.names = !dont_check_names)
} else if (is.data.frame(input_file)) {
x <- data.frame(input_file)
x <- data.frame(input_file, check.names = !dont_check_names)
} else if (is.vector(input_file)){
if(length(input_file) == 1){
if(!file.exists(input_file)){
stop("The file ", input_file, " does not exist! ")
}else{
if(dont_check_names){
x <- read.delim(input_file,
stringsAsFactors = FALSE)
}else{
x <- read.delim(input_file,
stringsAsFactors = FALSE,
check.names = FALSE)
}

x <- read.delim(input_file,
stringsAsFactors = FALSE,
check.names = !dont_check_names)
}
}else{
stop("The input object is not valid")
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2 changes: 1 addition & 1 deletion R/protein2SiteConversion.R
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ then make the argument 'overwrite_evidence = TRUE'")
## map mod sites in data to index
if(verbose) message("--- OPENING EVIDENCE FILE ")
## read in maxq. data
maxq_data <- .artms_checkIfFile(evidence_file, dont_check_names = FALSE)
maxq_data <- .artms_checkIfFile(evidence_file, dont_check_names = TRUE)
maxq_data <- as.data.table(maxq_data)

# Check maxquant version:
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