peakPantheR 1.0.0
Package: peakPantheR
Authors: Arnaud Wolfer
The peakPantheR
package is designed for the detection, integration and
reporting of pre-defined features in MS files (e.g. compounds, fragments,
adducts, …).
The Parallel Annotation is set to detect and integrate multiple compounds in multiple files in parallel and store results in a single object. It can be employed to integrate a large number of expected features across a dataset.
Using the faahKO raw MS dataset as an example, this vignette will:
Parallel compound integration is set to process multiple compounds in multiple files in parallel, and store results in a single object.
To acheive this, peakPantheR
will:
Diagram of the workflow and functions used for parallel annotation.
We can target 2 pre-defined features in 6 raw MS spectra file from the
faahKO package using peakPantheR_parallelAnnotation()
. For more
details on the installation and input data employed, please consult the
Getting Started with peakPantheR vignette.
First the paths to 3 MS file from the faahKO are located and used as input spectras. In this example these 3 samples are considered as representative of the whole run (e.g. Quality Control samples):
library(faahKO)
## file paths
input_spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
system.file('cdf/KO/ko16.CDF', package = "faahKO"),
system.file('cdf/KO/ko18.CDF', package = "faahKO"))
input_spectraPaths
#> [1] "/home/biocbuild/bbs-3.10-bioc/R/library/faahKO/cdf/KO/ko15.CDF"
#> [2] "/home/biocbuild/bbs-3.10-bioc/R/library/faahKO/cdf/KO/ko16.CDF"
#> [3] "/home/biocbuild/bbs-3.10-bioc/R/library/faahKO/cdf/KO/ko18.CDF"
Two targeted features (e.g. compounds, fragments, adducts, …) are defined and stored in a table with as columns:
cpdID
(numeric)cpdName
(character)