Re-factor derecksLabTools::combatRNAseq; requires library("ggfortify")

[dereckmezquita]

BUG: note at the moment you have to call library("ggfortify") before you can use this.

Usage:

temp1 <- data.table::fread("./data/20220221-stat1-in-NK-maturation.featureCounts-genes.csv")
temp2 <- data.table::fread("./data/LS_20210512-matrix.csv")

library("ggfortify")

# TODO rewrite the autoplot function

batch_corrected <- derecksLabTools::combatRNAseq(batches = list(temp1, temp2))

pdf("./combat-seq-batch-correction.pdf", width = 10, height = 10)
batch_corrected@qc_plots
dev.off()

data.table::fwrite(batch_corrected@corrected, "./data/combatseq-20220221-stat1-in-NK-maturation-LS_20210512.csv")