Perform 2 group analysis with visualization
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.
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
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