filter_masic_data: Filtering MASIC Data

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

Description

Filtering MASIC data by InterferenceScore and S/N of individual channels. Note, function in its current form also drops 40 columns out of the data.frame. E.g. for TMT10 the table contains 62 columns. After filtering, the left columns are 10 TMT channels, dataset and scan.

Usage

filter_masic_data(x, interference_score_threshold = 0.9, s2n_threshold = 4)

Arguments

x	(data.frame) collated MASIC output
s2n_threshold	(numeric) S/N calculated by vendor and extracted MASIC from raw files. Default is 4.
interference_scrore_threshold	(numeric) fetch extra metrics that MASIC extracts from dataset or not. Higher the number, the cleaner parent ion at MS1 level. Default is 0.9.

Details

Default values interference_score_threshold = 0.9 and s2n_threshold = 4 are fairly stringent. The least recomended setting is interference_score_threshold = 0.5 and s2n_threshold = 0. If not filtering intended do filter_masic_data(x,0,0) call.

Value

(data.frame) filtered MASIC output

Examples

path_to_MASIC_results <- system.file("extdata/global/masic_output", package = "PlexedPiperTestData")
x <- read_masic_data(path_to_MASIC_results, extra_metrics=TRUE)
dim(x)
x1 <- filter_masic_data(x,0,0)
dim(x1)
x2 <- filter_masic_data(x)
dim(x2)

vladpetyuk/PlexedPiper documentation built on June 24, 2021, 8:59 a.m.