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Read peak lists

Source: R/read_peaklist.R
read_peaklist.Rd

Reads peak lists from specified folders or vector of paths.

Usage

read_peaklist(
  paths,
  find_files,
  format_in = c("chemstation", "shimadzu_fid", "shimadzu_dad", "shimadzu_lcd",
    "shimadzu_gcd", "chromatotec", "asm", "cdf", "openlab"),
  pattern = NULL,
  peaktable_format = c("chromatographr", "original"),
  metadata_format = c("chromconverter", "raw"),
  read_metadata = TRUE,
  progress_bar,
  cl = 1,
  sort_by = c("auto", "none", "acquisition_time", "file_time"),
  data_format = NULL
)

Arguments

paths

Paths to files or folders containing peak list files.

find_files

Logical. Whether to treat the supplied paths as directories to search for files. Inferred if not supplied, by testing whether every path is a file.

format_in

Format of files to be imported/converted. One of chemstation (the default), shimadzu_fid, shimadzu_dad, shimadzu_lcd, shimadzu_gcd, chromatotec, asm, cdf (ANDI chrom) or openlab ('Agilent OpenLab CDS' .rx files, named by signal from the .acaml file beside them).

pattern

A pattern (e.g. a file extension). Defaults to NULL, in which case the file extension will be deduced from format_in.

peaktable_format

Whether to return peak tables in the standard chromatographr layout (the default) or with all the columns the file provides (original). A chromatographr table has the columns rt, start, end, area, height and FWHM (the full width at half maximum), with times in the same unit as the format's chromatograms and NA where the file does not record a value.

metadata_format

Format to output metadata. Either chromconverter (standardized field names) or raw (vendor field names, unmapped).

read_metadata

Logical. Whether to attach metadata. Defaults to TRUE.

progress_bar

Logical. Whether to show progress bar. Defaults to TRUE if pbapply is installed.

cl

Argument to pbapply specifying the number of parallel workers to use or a cluster object created by makeCluster (a set of parallel R worker processes). Defaults to 1.

sort_by

How to sort the samples: auto (default) sorts files by acquisition time unless paths lists the files explicitly or any acquisition time is missing; none keeps files in the order given, or in alphabetical order if find_files = TRUE; acquisition_time sorts by the acquisition time recorded in each file (run_datetime); file_time sorts by the time when each file was last modified.

data_format

Deprecated. Use peaktable_format instead.

Value

A peak_list: a list with one element per sample, holding its peak table, or a list of peak tables where the file records more than one. The tables are named by wavelength (e.g. "254") where the file records one, and otherwise by the file's own name for the signal; a table identical to another at the same wavelength is a copy and is left out. Each row is a peak. Every table starts with a sample column and a lambda column giving the signal's wavelength, which is NA for a detector without one or a file that does not record it, followed by the columns of peaktable_format.

Author

Ethan Bass

Examples

path <- system.file("extdata", "benzoxazinoid_standards",
                    package = "chromConverter")
peak_list <- read_peaklist(path, progress_bar = FALSE)
names(peak_list)
#>  [1] "MEOH"            "BENZOS_1000PPM"  "BENZOS_500PPM"   "BENZOS_250PPM"  
#>  [5] "BENZOS_125PPM"   "BENZOS_62,5PPM"  "BENZOS_31,25PPM" "BENZOS_16PPM"   
#>  [9] "BENZOS_8PPM"     "BENZOS_4PPM"    
peak_list[["BENZOS_250PPM"]][["254"]]
#>           sample lambda     rt start end        area    height   FWHM
#> 1  BENZOS_250PPM    254  1.948    NA  NA   140.95924   7.07890 0.2483
#> 2  BENZOS_250PPM    254  2.373    NA  NA   161.74519  14.59622 0.1433
#> 3  BENZOS_250PPM    254  2.517    NA  NA   108.11900  16.77651 0.0912
#> 4  BENZOS_250PPM    254  2.669    NA  NA   102.54382  21.65732 0.0752
#> 5  BENZOS_250PPM    254  2.769    NA  NA   389.25211  31.26716 0.1612
#> 6  BENZOS_250PPM    254  3.898    NA  NA  1211.76770  18.42384 0.7973
#> 7  BENZOS_250PPM    254  5.063    NA  NA   382.35251  11.64398 0.4211
#> 8  BENZOS_250PPM    254  5.319    NA  NA   160.09975  10.35239 0.2244
#> 9  BENZOS_250PPM    254  5.615    NA  NA   192.40610   9.96399 0.2633
#> 10 BENZOS_250PPM    254  6.108    NA  NA   335.43140   9.27820 0.4398
#> 11 BENZOS_250PPM    254  6.621    NA  NA   283.18048   7.90439 0.4360
#> 12 BENZOS_250PPM    254  7.223    NA  NA   158.82758   6.81299 0.3060
#> 13 BENZOS_250PPM    254  7.916    NA  NA   356.50873   5.75635 0.7946
#> 14 BENZOS_250PPM    254 12.541    NA  NA  7078.15283 349.55142 0.3142
#> 15 BENZOS_250PPM    254 14.203    NA  NA   136.62770   2.82697 0.6119
#> 16 BENZOS_250PPM    254 17.754    NA  NA    78.47887   2.87611 0.4023
#> 17 BENZOS_250PPM    254 19.068    NA  NA 10954.20000 456.22156 0.3721
#> 18 BENZOS_250PPM    254 20.979    NA  NA  1806.64539  76.05057 0.3652
#> 19 BENZOS_250PPM    254 28.225    NA  NA   637.83038  27.49332 0.3587
#> 20 BENZOS_250PPM    254 36.643    NA  NA    61.25155   1.62191 0.5246