batchQC {BatchQC} | R Documentation

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

### 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)

[Package BatchQC version 1.16.3 Index]