Filtering MASIC Data

Filtering MASIC data by interference score and signal-to-noise ratio (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 remaining columns are the 10 TMT channels, Dataset, and ScanNumber.

Usage

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

Arguments

x

(data.frame) collated MASIC output

interference_score_threshold

(numeric) The interference score reflects the proportion of the ion population isolated for fragmentation that is due to the targeted ion. 1 - InferferenceScore is due to co-isolated species. The higher the interference score, the cleaner the parent ion at the MS1 level. Default is 0.9.

s2n_threshold

(numeric) S/N calculated by vendor and extracted MASIC from raw files. Default is 4.

Value

(data.frame) filtered MASIC output

Details

Default values interference_score_threshold = 0.9 and s2n_threshold = 4 are fairly stringent. We recommend at least setting interference_score_threshold = 0.5 and s2n_threshold = 0. If filtering is not intended, use filter_masic_data(x,0,0).

Examples

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