Translate sample names to sample types — translate_sample_names_to_sample

Function translates sample names to sample types based on the sample name from Luminex file and the sample name from the layout file, which may not be provided. The function uses regular expressions to match the sample names to the sample types.

Usage

translate_sample_names_to_sample_types(
  sample_names,
  sample_names_from_layout = NULL
)

Arguments

sample_names: (character())
Vector of sample names from Luminex file
sample_names_from_layout: (character())
Vector of sample names from Layout file values in this vector may be different than sample_names and may contain additional information about the sample type like dilution. This vector when set has to have at least the length of sample_names.

Value

A vector of valid sample_type strings of length equal to the length of sample_names

Details

Function assigns SampleType to each of the samples from one of c(ALL, BLANK, TEST, NEGATIVE CONTROL, STANDARD CURVE, POSITIVE CONTROL).

It parses the names as follows:

If sample_names or sample_names_from_layout equals to BLANK, BACKGROUND or B, then SampleType equals to BLANK

If sample_names or sample_names_from_layout equals to STANDARD CURVE, SC, S, contains substring 1/\d+ and has prefix , S_, S , S or CP3, then SampleType equals to STANDARD CURVE. For instance, sample with a name S_1/2 or S 1/2 will be classified as STANDARD CURVE.

If sample_names or sample_names_from_layout equals to NEGATIVE CONTROL, N, or contains substring NEG, then SampleType equals to NEGATIVE CONTROL

If sample_names or sample_names_from_layout starts with P followed by whitespace, POS followed by whitespace, some sample name followed by substring 1/\d+ SampleType equals to POSITIVE CONTROL

Otherwise, the returned SampleType is TEST

It also removes any additional suffixes created by make.unique() method, such as, .1, .4.

Examples

translate_sample_names_to_sample_types(c("B", "BLANK", "NEG", "TEST1"))
#> [1] "BLANK"            "BLANK"            "NEGATIVE CONTROL" "TEST"            
translate_sample_names_to_sample_types(c("S", "CP3"))
#> [1] "STANDARD CURVE" "TEST"