Checks Expression and Metadata for Adding to GXPA — check_files_for

Performs common checks on the expression data and metadata files. Often run before adding to GXPA

Usage

check_files_for_GXPA(expr_file, samples_file)

expr_file: expression data file name, with path, to check with metadata
samples_file: metadata data file name, with path, to check with expression data

message indicating all checks passed

The following check are performed:

number of columns of expression data not equal to number of rows in metadata
check for entirely quoted column names or row names in expr file
duplicated expression data column names
duplicated metadata values in first column
expression data column names that can't link to metadata samples
- Will give warning if linking is possible but currently not matching order
duplicated gene names (ignoring case)
first column name of metadata must be an empty string of _id
other column names of metadata must follow standard R variable naming convention

if (FALSE) { # \dontrun{
check_files_for_GXPA(
  expr_file = "expr.expr.txt",
  samples_file = "expr.samples.csv"
)
} # }