MetaCellFiltering: Filter lines in the matrix of intensities w.r.t. some...

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

Filter lines in the matrix of intensities w.r.t. some criteria

Description

#' Filters the lines of Biobase::exprs() table with conditions on the number of missing values. The user chooses the minimum amount of intensities that is acceptable and the filter delete lines that do not respect this condition. The condition may be on the whole line or condition by condition.

The different methods are : "WholeMatrix": given a threshold th, only the lines that contain at least th values are kept. "AllCond": given a threshold th, only the lines which contain at least th values for each of the conditions are kept. "AtLeastOneCond": given a threshold th, only the lines that contain at least th values, and for at least one condition, are kept.

Usage

MetaCellFiltering(obj, indices, cmd, processText = "")

Arguments

obj	An object of class MSnSet containing quantitative data.
indices	A vector of integers which are the indices of lines to keep.
cmd	xxxx. Available values are: 'delete', 'keep'.
processText	A string to be included in the MSnSet object for log.

Value

An instance of class MSnSet that have been filtered.

Author(s)

Florence Combes, Samuel Wieczorek

Examples

data(Exp1_R25_pept, package="DAPARdata")
obj <- Exp1_R25_pept[seq_len(100)]
level <- 'peptide'

#' 
#' Delete lines which are entirely filled with any missing values ('Missing MEC' and 'Missing POV')
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), level)
indices <- GetIndices_WholeLine(metacell.mask)
obj.filter <- MetaCellFiltering(obj, indices, "delete")


obj <- obj[1:10]

pattern <- "Quantified"
type <- "AtLeastOneCond"
percent <- FALSE
op <- ">="
th <- 3
indices <- GetIndices_MetacellFiltering(obj, level, pattern, type, percent, op, th)
obj <- MetaCellFiltering(obj, indices, "keep")$new
#fData(obj)[, obj@experimentData@other$names_metacell]

pattern <- "Quant. by direct id"
type <- "AtLeastOneCond"
percent <- FALSE
op <- ">="
th <- 3
indices <- GetIndices_MetacellFiltering(obj, level, pattern, type, percent, op, th)
obj <- MetaCellFiltering(obj, indices, "keep")$new
#fData(obj)[, obj@experimentData@other$names_metacell]
names.1 <- rownames(obj)


obj <- Exp1_R25_pept[seq_len(100)]
pattern <- "Quant. by direct id"
type <- "AtLeastOneCond"
percent <- FALSE
op <- ">="
th <- 3
indices <- GetIndices_MetacellFiltering(obj, level, pattern, type, percent, op, th)
obj <- MetaCellFiltering(obj, indices, "keep")$new
#fData(obj)[, obj@experimentData@other$names_metacell]

pattern <- "Quantified"
type <- "AtLeastOneCond"
percent <- FALSE
op <- ">="
th <- 3
indices <- GetIndices_MetacellFiltering(obj, level, pattern, type, percent, op, th)
obj <- MetaCellFiltering(obj, indices, "keep")$new
#fData(obj)[, obj@experimentData@other$names_metacell]
names.2 <- rownames(obj)

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