outlierFind_i: Find outlier spectra within a protein or pedtide i.

In mooredf22/protlocassign: Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

Find outlier spectra within a protein or pedtide i.

Description

Service function for outlierFind (see help function for outlierFind).

Usage

outlierFind_i(
  i,
  protClass,
  outlierLevel = "peptide",
  numRefCols,
  numDataCols,
  outlierMeth,
  range,
  proba,
  eps = eps,
  randomError
)

Arguments

i	unique identifier for protein i
protClass	a data frame containing profiles associated with either spectra or peptides (see Tutorial 6)
outlierLevel	'peptide' for outlier spectra within peptides, or 'protein' for outlier peptides within proteins
numRefCols	number of columns (variables) before data columns
numDataCols	number of fractions in each profile
outlierMeth	boxplot (recommended), scores, or none (if no outliers are to be reported)
range	the range parameter used for identifying outliers using the boxplot method
proba	probability to exclude outlier for scores method
eps	small value to add so that log argument is greater than zero
randomError	TRUE if allow it to be random

Value

New data frame for a single protein or peptide with an additional column that indicates the number of fractions in a profile (peptides or spectra) that are outliers

Examples

set.seed(63561)
eps <- 0.029885209
data(spectraNSA_test)
uniqueLabel <- spectraNSA_test$pepId[1]
flagSpectraBox_i <- outlierFind_i(i=uniqueLabel, protClass=spectraNSA_test,
                      outlierLevel='peptide', numRefCols=5, numDataCols=9,
                      outlierMeth='boxplot', range=3, proba=NA, eps=eps,
                      randomError=TRUE)
str(flagSpectraBox_i)

mooredf22/protlocassign documentation built on Sept. 13, 2023, 3:57 p.m.