validPEAKGR: Validate a peak-group-of-interest by performing a...
In lauzikaite/massFlowR: LC-MS Data Pre-Processing

View source: R/functions-validPEAKS_helpers.R

Functions correlates all peaks of a peak-groups across all samples in which they were detected. Obtained Pearson correlation coefficients are used to build a peak-peak network with pairs above selected correlation threshold. igraph Cluster Label Propagation algorithm is used to detect communities of peaks with the network. These communities are returned as independent peak-goups, or, Pseudo Chemical Spectra.

1	validPEAKGR(pkg, pkg_ints, out_dir, cor_thr, min_samples_n, save_plot = FALSE)

`pkg`	`numeric` specifying a peak-group-of-interest.
`pkg_ints`	`data.frame` with centWave values for the peak-group-of-interest.
`out_dir`	`character` specifying desired directory for output, if plotting is selected.
`cor_thr`	`numeric` defining Pearson correlation coefficient threshold for inter-sample correlation between peaks.
`min_samples_n`	`numeric` specifying the minimum number of samples in which peak has to be detected in order to be considered.
`save_plot`	`logical` whether network plot should be saved as a pdf file in the out_dir, default set to FALSE.

Function returns a list for every community into which peak-group was split to by the Cluster Label Propagation algorithm. Each element of the returned list contains centWave values for every community peak in the samples in which it was detected.

lauzikaite/massFlowR documentation built on April 29, 2020, 9:45 a.m.