Man pages for Bioconductor-mirror/BatchQC
Batch Effects Quality Control Software

batchQCChecks for presence of batch effect and creates a html report...
batchQC_analyzeChecks for presence of batch effect and reports whether the...
batchqc_circosplotProduce Circos plot
batchQC_condition_adjustedReturns adjusted data after remove the variation across...
batchqc_correlationProduce correlation heatmap plot
batchqc_corscatterProduce Median Correlation plot
batchqc_explained_variationReturns a list of explained variation by batch and condition...
batchQC_filter_genesReturns a datset after filtering genes of zero variance...
batchQC_fsva_adjustedUse frozen surrogate variable analysis to remove the...
batchqc_heatmapProduce heatmap plots for the given data
batchQC_num.svReturns the number of surrogate variables to estimate in the...
BatchQCout-classThe BatchQC output class to output BatchQC results
batchqc_pcaPerforms principal component analysis and produces plot of...
batchqc_pca_svdPerforms PCA svd variance decomposition and produces plot of...
batchqc_pc_explained_variationReturns explained variation for each principal components
batchQC_shapeVariationPerform Mean and Variance batch variation analysis
batchQC_svaEstimate the surrogate variables using the 2 step approach...
batchQC_svregress_adjustedRegress the surrogate variables out of the expression data
batchtestPerforms test to check whether batch needs to be adjusted
combatPlotAdjust for batch effects using an empirical Bayes framework...
example_batchqc_dataBatch and Condition indicator for signature data captured...
getShinyInputGetter function to get the shinyInput option
getShinyInputCombatGetter function to get the shinyInputCombat option
getShinyInputOrigGetter function to get the shinyInputOrig option
getShinyInputSVAGetter function to get the shinyInputSVA option
getShinyInputSVAfGetter function to get the shinyInputSVAf option
getShinyInputSVArGetter function to get the shinyInputSVAr option
gnormalizePerform Genewise Normalization of the given data matrix
log2CPMCompute log2(counts per mil reads) and library size for each...
makeSVDCompute singular value decomposition
pcResCompute variance of each principal component and how they...
plotPCPlot first 2 principal components
protein_example_dataBatch and Condition indicator for protein expression data
rnaseq_simGenerate simulated count data with batch effects for ngenes
setShinyInputSetter function to set the shinyInput option
setShinyInputCombatSetter function to set the shinyInputCombat option
setShinyInputOrigSetter function to set the shinyInputOrig option
setShinyInputSVASetter function to set the shinyInputSVA option
setShinyInputSVAfSetter function to set the shinyInputSVAf option
setShinyInputSVArSetter function to set the shinyInputSVAr option
Bioconductor-mirror/BatchQC documentation built on May 29, 2017, 12:06 a.m.