Add metadata to a list of chromatograms

Attaches the columns of a table to the chromatograms of a chrom_list as metadata fields, matching each row to a sample by name. The new fields can then be used by subset.chrom_list and requested from extract_metadata. Where an element holds several chromatograms, such as the traces read_agilent_d returns for each .D directory, every one of them gets the sample's values.

Usage

add_metadata(chrom_list, metadata, by = "name", overwrite = FALSE)

Arguments

chrom_list

A chrom_list object.

metadata

A data.frame, tibble or data.table with one row per sample.

by

The column of metadata holding the sample names, matched to names(chrom_list). Defaults to name, the column extract_metadata identifies samples by.

overwrite

Whether a column may replace a field that chromConverter reads from the file, such as sample_name. Defaults to FALSE, in which case such a column is an error.

Value

chrom_list with the columns of metadata attached to its chromatograms, and their names recorded in an added_metadata attribute, from which chromatographR's get_peaktable fills its sample_meta. A sample without a row in metadata is left unchanged, with a warning.

See also

extract_metadata, subset.chrom_list

Examples

path <- system.file("extdata/ladder.txt", package = "chromConverter")
chrom <- read_chroms(path, format_in = "shimadzu_ascii",
                     find_files = FALSE, progress_bar = FALSE)
# three copies stand in for the samples of a sequence
chroms <- c(chrom, chrom, chrom)
names(chroms) <- c("s1", "s2", "s3")
meta <- data.frame(name = c("s1", "s2", "s3"),
                   treatment = c("control", "drought", "drought"))
chroms <- add_metadata(chroms, meta)
extract_metadata(chroms, what = "treatment")
#>   name treatment
#> 1   s1   control
#> 2   s2   drought
#> 3   s3   drought
names(subset(chroms, treatment == "drought"))
#> [1] "s2" "s3"