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Read and convert an Agilent MassHunter Quant CSV result file

Source: R/read_msdata.R
read_MassHunterCSV.Rd

Read and convert an Agilent MassHunter Quant CSV result file

Usage

read_MassHunterCSV(filename, silent = FALSE)

Arguments

filename

File path of MassHunter Quant CSV file

silent

Suppress messages

Value

A tibble in the long format

Examples

library(SLINGtools)

data_file_path <- system.file("extdata",
  "Testdata_Lipidomics_MHQuant_Detailed.csv", package = "SLINGtools")
d <- read_MassHunterCSV(data_file_path)
#> Reading [Testdata_Lipidomics_MHQuant_Detailed.csv] ...
#> Imported 215 samples with 428 transitions. 
d
#> # A tibble: 92,020 × 16
#>    RUN_ID DataFile…¹ ANALY…² DataN…³ Sampl…⁴ AcqTimeStamp        VialP…⁵ FEATU…⁶
#>     <int> <chr>      <chr>   <chr>   <chr>   <dttm>              <chr>   <chr>  
#>  1      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 14:0
#>  2      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 15:0
#>  3      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 16:0
#>  4      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 16:1
#>  5      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 16:2
#>  6      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 17:0
#>  7      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 17:1
#>  8      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 18:0
#>  9      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 18:1
#> 10      1 001_EQC_T… 001_EQ… 001_EQ… Sample  2018-04-12 18:28:00 Vial 2  CE 18:…
#> # … with 92,010 more rows, 8 more variables: IonPolarity <fct>,
#> #   PrecursorMZ <dbl>, ProductMZ <dbl>, CollisionEnergy <dbl>, RT <dbl>,
#> #   Area <dbl>, FWHM <dbl>, MI <lgl>, and abbreviated variable names
#> #   ¹​DataFileName, ²​ANALYSIS_ID, ³​DataName, ⁴​SampleType, ⁵​VialPosition,
#> #   ⁶​FEATURE_NAME