README.md

In luechtian/lipidcountr: Quantify Mass Spectrometric Outputs Of Lipid Spectra

lipidcountr

The goal of lipidcountr is to streamline and simplify the quantification step of the lipidomics workflow in the Bruegger lab.

Installation

You can install lipidcountr from GitHub with:

# install.packages("devtools")
devtools::install_github("luechtian/lipidcountr")

Example

library(lipidcountr)

list.files(system.file("extdata", package = "lipidcountr"), pattern = ".txt", full.names = FALSE) %>% head()
#> [1] "yymmdd_XtrIL_ExampleData_CE.txt"     
#> [2] "yymmdd_XtrIL_ExampleData_Cer.txt"    
#> [3] "yymmdd_XtrIL_ExampleData_Chol.txt"   
#> [4] "yymmdd_XtrIL_ExampleData_DAG.txt"    
#> [5] "yymmdd_XtrIL_ExampleData_Hex2Cer.txt"
#> [6] "yymmdd_XtrIL_ExampleData_HexCer.txt"

read_lipidview_files(system.file("extdata", package = "lipidcountr"))
#> # A tibble: 16,682 x 6
#>    class mz    species scan_name        sample    intensity
#>    <chr> <chr> <chr>   <chr>            <chr>         <dbl>
#>  1 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_1  58161729.
#>  2 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_2  56223689.
#>  3 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_3  56113097.
#>  4 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_4  56459944.
#>  5 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_5  66408624.
#>  6 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_6  50757691.
#>  7 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_7  58787795.
#>  8 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_8  35023855.
#>  9 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_9  54665552.
#> 10 CE    544.6 IS 9:0  FA 20:0+C3H6O/CE sample_10 64823347.
#> # ... with 16,672 more rows

luechtian/lipidcountr documentation built on April 21, 2022, 12:36 a.m.