README.md

In jankinsan/BatchEC: Evaluates and corrects batch effects in gene expression data

BatchEC

An R package that evaluates batch effects in gene expression data and corrects batches using the ComBat algorithm (available in sva package).

Usage

install_github("jankinsan/BatchEC")

library(NMF)

library(BatchEC)

#if input is to be given as tab delimited text files

batch_corrected_dataset <- BatchEC_file( exprFile = "~filepath.txt", batchFile = "~filepath2.txt", batch, NameString = "project_name", discrete.batch = TRUE, clus.method=c("NMF", "km"))

#if input objects already exist in the R environment

batch_corrected_dataset <- BatchEC(expr= expression_dataset, batch.info, batch ="batch_title", NameString = "project_or_file_name", discrete.batch = TRUE, clus.method=c("NMF", "km")) where expr1 is gene expression data; rows should be genes and columns should be samples.

Functions

BatchEC_file Batch effects evaluation and correction from files. Both the files (containing the Expression data and the batch information should be tab-delimited text files.)

BatchEC Batch effects evaluation and correction from objects loaded in the workspace.

boxplot_data Plots boxplots showing Gene Expression across samples

ComBat_data Batch Correction using ComBat

correlationPlot Correlation Scatter Plot

kmeans_PCA PCA plot with k-means information

lin_reg Linear Regression of Principal Components

pca_batch PCA Plot with batch information

pca_prop_var PCA Proportion of Variation

jankinsan/BatchEC documentation built on Sept. 9, 2021, 8:12 p.m.