GetIndices_MetacellFiltering: Delete the lines in the matrix of intensities and the...

In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Delete the lines in the matrix of intensities and the metadata table given their indice.

Description

Delete the lines in the matrix of intensities and the metadata table given their indice.

Usage

GetIndices_MetacellFiltering(
  obj,
  level,
  pattern = NULL,
  type = NULL,
  percent,
  op,
  th
)

Arguments

obj	An object of class MSnSet containing quantitative data.
level	A vector of integers which are the indices of lines to delete.
pattern	A string to be included in the MSnSet object for log.
type	xxx
percent	xxx
op	xxx
th	xxx

Value

An instance of class MSnSet that have been filtered.

Author(s)

Samuel Wieczorek

Examples

data(Exp1_R25_pept, package="DAPARdata")
obj <- Exp1_R25_pept[seq_len(10)]
level <- GetTypeofData(obj)
pattern <- c("Missing", "Missing POV")
type <- "AtLeastOneCond"
percent <- FALSE
op <- ">="
th <- 1
indices <- GetIndices_MetacellFiltering(obj, level, pattern, type, percent, op, th)



pattern <- "Quantified"
type <- "AtLeastOneCond"
percent <- FALSE
op <- ">="
th <- 4
indices2.1 <- GetIndices_MetacellFiltering(obj, level, pattern, type, percent, op, th)

pattern <- "Quant. by direct id"
type <- "AtLeastOneCond"
percent <- FALSE
op <- ">="
th <- 3
indices2.2 <- GetIndices_MetacellFiltering(obj, level, pattern, type, percent, op, th)

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.