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

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Description

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

Usage

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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

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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)

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