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
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)
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 |
outputfile Report file generated by batchQC
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)