Man pages for symbioticMe/proBatch
Tools for Batch Effects Diagnostics and Correction

adjust_batch_trendadjust batch signal trend with the custom (continuous) fit
color_list_to_dfColor list to data frame
correct_batchCorrection of batch effects in the data
correct_with_ComBatStandardized input-output ComBat normalization ComBat allows...
create_peptide_annotationPrepare peptide annotation from long format data frame Create...
dates_to_posixConvert data/time to POSIXct
date_to_sample_orderConvert date/time to POSIXct and rank samples by it
example_peptide_annotationPeptide annotation data
example_proteomeExample protein data in long format
example_proteome_matrixExample protein data in matrix
example_sample_annotationSample annotation data version 1
fit_nonlinearFit a non-linear trend
generate_colors_for_numericGenerates color list
get_peptide_corr_dfTransform square correlation matrix into long data frame of...
get_sample_corr_distribCalculates correlation distribution for all pairs of the...
log_transformLog transformation of the data, ensuring that the row and...
long_to_matrixLong to wide conversion
matrix_to_longWide to long conversion
merge_rare_levelsReplaces rare levels with other
normalizeData normalization methods
normalize_dataNormalization brings the samples to the same scale
normalize_sample_mediansNormalization by centering sample medians to global median of...
plot_corr_matrixVisualise correlation matrix
plot_heatmapPlot the heatmap of samples
plot_hierarchical_clusteringcluster the data matrix to visually inspect which confounder...
plot_iRTPlot iRT measurements
plot_PCAplot PCA plot
plot_peptide_corr_distributionPlot distribution of peptide correlations within one protein...
plot_peptides_of_one_proteinPlot peptides of one protein
plot_protein_corrplotPeptide correlation matrix (heatmap)
plot_PVCAPlot variance distribution by variable
plot_sample_corr_distributionCreate violin plot of correlation distribution
plot_sample_corr_heatmapSample correlation matrix (heatmap)
plot_sample_mean_or_boxplotPlot per-sample mean or boxplot (showing median and...
plot_single_featurePlot peptide measurements
plot_spike_inPlot spike-in measurements
plot_with_fitting_curvePlot peptide measurements across multi-step analysis
proBatchproBatch: A package for diagnostics and correction of batch...
quantile_normalizeQuantile normalization of the data, ensuring that the row and...
sample_annotation_to_colorsGenerate colors for sample annotation
symbioticMe/proBatch documentation built on Jan. 22, 2019, 5:17 p.m.