clean_profile: Preprocess a co-elution profile

In fosterlab/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)

fosterlab/PrInCE documentation built on Dec. 13, 2020, 5:50 a.m.