clean_profiles {PrInCE} | R Documentation

## Preprocess a co-elution profile matrix

### Description

Clean a matrix of co-elution/co-fractionation profiles 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_profiles(profile_matrix, impute_NA = TRUE, smooth = TRUE,
      smooth_width = 4, noise_floor = 0.001)

### Arguments

`profile_matrix` | a numeric matrix of co-elution profiles, with proteins in rows, or a `MSnSet` object
`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 matrix

### Examples

    data(scott)
    mat <- scott[c(1, 16), ]
    mat_clean <- clean_profiles(mat)

[Package PrInCE version 1.0.1 Index]