# Batch Effects Quality Control Software

## Documentation for package ‘BatchQC’ version 1.8.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

batchQC | Checks for presence of batch effect and creates a html report with information including whether the batch needs to be adjusted
BatchQCout-class | The BatchQC output class to output BatchQC results
batchQC_analyze | Checks for presence of batch effect and reports whether the batch needs to be adjusted
batchqc_circosplot | Produce Circos plot
batchQC_condition_adjusted | Returns adjusted data after remove the variation across conditions
batchqc_correlation | Produce correlation heatmap plot
batchqc_corscatter | Produce Median Correlation plot
batchqc_explained_variation | Returns a list of explained variation by batch and condition combinations
batchQC_filter_genes | Returns a datset after filtering genes of zero variance across batch and condition combinations
batchQC_fsva_adjusted | Use frozen surrogate variable analysis to remove the surrogate variables inferred from sva
batchqc_heatmap | Produce heatmap plots for the given data
batchQC_num.sv | Returns the number of surrogate variables to estimate in the model using a permutation based procedure
batchqc_pca | Performs principal component analysis and produces plot of the first two principal components
batchqc_pca_svd | Performs PCA svd variance decomposition and produces plot of the first two principal components
batchqc_pc_explained_variation | Returns explained variation for each principal components
batchQC_shapeVariation | Perform Mean and Variance batch variation analysis
batchQC_sva | Estimate the surrogate variables using the 2 step approach proposed by Leek and Storey 2007
batchQC_svregress_adjusted | Regress the surrogate variables out of the expression data
batchtest | Performs test to check whether batch needs to be adjusted
batch_indicator | Batch and Condition indicator for signature data captured when activating different growth pathway genes in human mammary epithelial cells.

combatPlot

Adjust for batch effects using an empirical Bayes framework ComBat allows users to adjust for batch effects in datasets where the batch covariate is known, using methodology described in Johnson et al. 2007. It uses either parametric or non-parametric empirical Bayes frameworks for adjusting data for batch effects. Users are returned an expression matrix that has been corrected for batch effects. The input data are assumed to be cleaned and normalized before batch effect removal.

example_batchqc_data | Batch and Condition indicator for signature data captured when activating different growth pathway genes in human mammary epithelial cells.
getShinyInput | Getter function to get the shinyInput option
getShinyInputCombat | Getter function to get the shinyInputCombat option
getShinyInputOrig | Getter function to get the shinyInputOrig option
getShinyInputSVA | Getter function to get the shinyInputSVA option
getShinyInputSVAf | Getter function to get the shinyInputSVAf option
getShinyInputSVAr | Getter function to get the shinyInputSVAr option
gnormalize | Perform Genewise Normalization of the given data matrix
lmFitC | Fit linear model for each gene given a series of arrays. This is the standard lmFit function from limma package with the modification to accept an additional correlation matrix parameter option
log2CPM | Compute log2(counts per mil reads) and library size for each sample
makeSVD | Compute singular value decomposition
pcRes | Compute variance of each principal component and how they correlate with batch and cond
plotPC | Plot first 2 principal components
plot_genewise_moments | Visualize gene-wise moments
plot_samplewise_moments | Visualize sample-wise moments
protein_data | Batch and Condition indicator for protein expression data
protein_example_data | Batch and Condition indicator for protein expression data
protein_sample_info | Batch and Condition indicator for protein expression data
rnaseq_sim | Generate simulated count data with batch effects for ngenes
setShinyInput | Setter function to set the shinyInput option
setShinyInputCombat | Setter function to set the shinyInputCombat option
setShinyInputOrig | Setter function to set the shinyInputOrig option
setShinyInputSVA | Setter function to set the shinyInputSVA option
setShinyInputSVAf | Setter function to set the shinyInputSVAf option
setShinyInputSVAr | Setter function to set the shinyInputSVAr option
signature_data | Batch and Condition indicator for signature data captured when activating different growth pathway genes in human mammary epithelial cells.