Man pages for statOmics/MSqRob
Robust statistical inference for quantitative LC-MS proteomics

addFactorInteractionsAdd a combination of two or more factor variables to a...
addVarFromVarAdd a variable to a protdata object based on an existing...
adjustNamesAdjust the names of the elements in a list of dataframes
countPeptidesCount the number of peptides in each group
cutOffPvalFind cut off for p-values enriched in values close to 1
df2protdataData frame to protein data
dummyVars_MSqRobCreate A Full Set of Dummy Variables
fdrtool_subsetEstimate (Local) False Discovery Rates For Diverse Test...
fit.modelFit peptide-based models
getAccessions-protdata-methodExtract the accession slot of a protdata object
getAccessions-protLM-methodExtract the accession slot of a protLM object
getAnnotations-protdata-methodExtract the annotation slot of a protdata object
getAnnotations-protLM-methodExtract the annotation slot of a protLM object
getBetaVcovDf-glmerMod-methodGet beta, vcov, df and sigma from a generalized linear mixed...
getBetaVcovDf-glm-methodGet beta, vcov, df and sigma from a generalized linear model
getBetaVcovDfListGet a list of beta, vcov, df and sigma from a protLM object
getBetaVcovDf-lmerMod-methodGet beta, vcov, df and sigma from a linear mixed model
getBetaVcovDf-lm-methodGet beta, vcov, df and sigma from an ordinary linear model
getData-protdata-methodExtract the data slot of a protdata object
getModels-protLM-methodExtract the model slot of a protLM object
getPData-protdata-methodExtract the annotation slot of a protdata object
get_qvalsAdjust P-values for Multiple Comparisons
getThetaVarsGet variances and degrees of freedom of model parameters
import2MSnSetImport a file in a prespecified format and convert it to an...
importDIADataImport data independent acquisition files
index2NumericConvert index to only numeric values
init_ann_MQ_ExcelInitialize an annotation Excel file based on a MaxQuant...
inspect_loads_MSqRobInspect the variables present in a data.frame from binary...
length-protdata-methodLength of a protdata object
length-protLM-methodLength of a protLM object
loads_MSqRobLoading only given variables of a data.frame from binary file
makeAnnotationCreate an annotation data frame
makeContrastCreate a contrast matrix
MSnSet2protdataMSnSet to protein data
pasteAnnotationAdd annotations to a data frame in "long" format
plot_fdrtoolMake diagnostic plots for fdrtool results
preprocess_genericPreprocess MSnSet objects originating from prespecified file...
preprocess_longPreprocess data in "long" format
preprocess_MaxQuantPreprocess MSnSet objects originating from MaxQuant...
preprocess_MSnSetPreprocess MSnSet objects
preprocess_widePreprocess data in "wide" format
protdata-classProtein Data Object - class
protLM-classProtein Linear Model Object - class
prot.p.adjustAdjust P-values for Multiple Comparisons
prot.p.adjust_protwiseAdjust P-values for Multiple Comparisons per Protein
prot.signifAssess significance of q-values and sort by significance
read2MSnSetImport a file and convert it to an MSnSet object
read_MaxQuantImport a MaxQuant peptides.txt file
read_moFFImport a peptides summary file produced by moFF
saves_MSqRobSave the variables of a data.frame in distinct binary files
selectAccessions-protdata-methodSelect accessions from a protdata object
setAccessions-protdata-methodChange the accession slot of a protdata object
setAccessions-protLM-methodChange the accession slot of a protLM object
setAnnotations-protdata-methodChange the annotation slot of a protdata object
setAnnotations-protLM-methodChange the annotation slot of a protLM object
setData-protdata-methodChange the data slot of a protdata object
setModels-protLM-methodChange the model slot of a protLM object
smallestUniqueGroupsSmallest unique protein groups
squeezeParsSqueeze variances and other parameters
squeezeThetasSqueeze variances and other parameters
squeezeVarRobRobustly Squeeze Sample Variances
sub-protdata-ANY-ANY-ANY-methodSelect elements from a protdata object
sub-protLM-ANY-ANY-ANY-methodSelect elements from a protLM object
test.ANOVAANOVA for multiple contrasts
test.contrastTest a contrast
test.contrast_adjustTest a contrast and perform FDR correction
test.contrast_stagewisePerform stage-wise contrast testing
test.protLMcontrastTest a contrast
update.lmerModUpdate lmerMod object with new thetas without changing the...
update_protLMUpdate protLM object with new parameter variances and...
statOmics/MSqRob documentation built on Nov. 19, 2017, 6:54 a.m.