Grp2Analysis-class: Perform 2 group analysis with visualization

Description Fields Methods

Description

Perform 2 group analysis with visualization

Fields

proteinIntensity

data.frame where colnames are Raw.File names, row.names are protein ID's and cells are protein abundances.

annotation_

annotations data.frame with columns such as Raw.File, Condition, Run etc.

proteinAnnotation

information about the proteins, nr of peptides etc.

nrPeptides

min number of peptides per protein

maxNA

maximum number of NA's

condition

summary of conditions

projectName

name of project

projectID

name of experiment

pvalue

pvalue threshold

qvalue

qvalue threshold

pfoldchange

foldchange threshold for p volcano plot

qfoldchange

foldchange threshold for q volcano plot

reference

document

removeDates

strip the date from file name.

Methods

getConditionData(condition)

get intensities as matrix for single condition

getModPValuesCI()

get Pvalues and confidence intervals

getNormalized()

return normalized data

getNormalizedGrpAverages()

computes grp averages per protein

getNrNAs()

return number of NAs per protein

getResultTableWithPseudo()

add pseudo p-values and pseudo fold changes

getResultTableWithPseudoAndClustering()

calls getResultTableWithPseudo() and adds clusterID column

setMQProteinGroups(MQProteinGroups)

set MQ protein groups table

setNormalizationMethod(normalizationMethod = "robustscale", housekeeper = "")

set the normalization parameters

setProteins(protein)

used to verify proteingroups structure and set members


protViz/SRMService documentation built on Nov. 13, 2021, 9:58 a.m.