batchQC: Checks for presence of batch effect and creates a html report...

In BatchQC: Batch Effects Quality Control Software

Description

Checks for presence of batch effect and creates a html report with information including whether the batch needs to be adjusted

Usage

batchQC(
  dat,
  batch,
  condition = NULL,
  report_file = "batchqc_report.html",
  report_dir = ".",
  report_option_binary = "111111111",
  view_report = FALSE,
  interactive = TRUE,
  batchqc_output = FALSE,
  log2cpm_transform = FALSE
)

Arguments

dat	Given data or simulated data from rnaseq_sim()
batch	Batch covariate
condition	Covariates or conditions of interest besides batch
report_file	Output report file name
report_dir	Output report directory path
report_option_binary	9 bits Binary String representing the plots to display and hide in the report
view_report	when TRUE, opens the report in a browser
interactive	when TRUE, opens the interactive shinyApp
batchqc_output	when TRUE, creates BatchQCout object in batchqc_output.rda R object file
log2cpm_transform	when TRUE, transforms the data using log2CPM - log2 Counts Per Million transformation function

Value

outputfile Report file generated by batchQC

Examples

nbatch <- 3
ncond <- 2
npercond <- 10
data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond=
    npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800, 
    basedisp=100, bdispstep=-10, swvar=1000, seed=1234)
batch <- rep(1:nbatch, each=ncond*npercond)
condition <- rep(rep(1:ncond, each=npercond), nbatch)
batchQC(data.matrix, batch=batch, condition=condition, view_report=FALSE, 
    interactive=FALSE)

BatchQC documentation built on Nov. 8, 2020, 8:30 p.m.