clean_profile: Preprocess a co-elution profile

In PrInCE: Predicting Interactomes from Co-Elution

Description

Clean a co-elution/co-fractionation profile by (1) imputing single missing values with the average of neighboring values, (2) replacing missing values with random, near-zero noise, and (3) smoothing with a moving average filter.

Usage

clean_profile(chromatogram, impute_NA = TRUE, smooth = TRUE,
  smooth_width = 4, noise_floor = 0.001)

Arguments

chromatogram	a numeric vector corresponding to the chromatogram trace
impute_NA	if true, impute single missing values with the average of neighboring values
smooth	if true, smooth the chromatogram with a moving average filter
smooth_width	width of the moving average filter, in fractions
noise_floor	mean value of the near-zero noise to add

Value

a cleaned profile

Examples

data(scott)
chrom <- scott[16, ]
cleaned <- clean_profile(chrom)

PrInCE documentation built on Nov. 8, 2020, 6:34 p.m.