Man pages for BatchQC
Batch Effects Quality Control Software
| batchQC | Checks for presence of batch effect and creates a html report... |
| batchQC_analyze | Checks for presence of batch effect and reports whether the... |
| batchqc_circosplot | Produce Circos plot |
| batchQC_condition_adjusted | Returns adjusted data after remove the variation across... |
| 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... |
| batchQC_filter_genes | Returns a datset after filtering genes of zero variance... |
| batchQC_fsva_adjusted | Use frozen surrogate variable analysis to remove the... |
| batchqc_heatmap | Produce heatmap plots for the given data |
| batchQC_num.sv | Returns the number of surrogate variables to estimate in the... |
| BatchQCout-class | The BatchQC output class to output BatchQC results |
| batchqc_pca | Performs principal component analysis and produces plot of... |
| batchqc_pca_svd | Performs PCA svd variance decomposition and produces plot of... |
| 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... |
| batchQC_svregress_adjusted | Regress the surrogate variables out of the expression data |
| batchtest | Performs test to check whether batch needs to be adjusted |
| combatPlot | Adjust for batch effects using an empirical Bayes framework... |
| example_batchqc_data | Batch and Condition indicator for signature data captured... |
| 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.... |
| log2CPM | Compute log2(counts per mil reads) and library size for each... |
| makeSVD | Compute singular value decomposition |
| pcRes | Compute variance of each principal component and how they... |
| plot_genewise_moments | Visualize gene-wise moments |
| plotPC | Plot first 2 principal components |
| plot_samplewise_moments | Visualize sample-wise moments |
| protein_example_data | 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 |
