plot diagnostics before and after process_data()

plot diagnostics before and after process_data()

plot_diagnostics(expr1, expr2, group_col, abl = 2)

Arguments

expr1

expression matrix 1 for original data

expr2

expression matrix 2 for processed data

group_col

vector of group of samples

abl

num, cutoff line

Value

multiple plots

Examples

data("im_data_6")
dge <- edgeR::DGEList(
  counts = Biobase::exprs(im_data_6),
  samples = Biobase::pData(im_data_6)
)
dge$logCPM <- edgeR::cpm(dge, log = TRUE)
proc_data <- process_data(dge,
  group_col = "celltype.ch1",
  target_group = "NK"
)
#>        NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
#> Down             4009         3944       3146   2694   2153
#> NotSig           1476         2678       4405   4985   6183
#> Up               4926         3789       2860   2732   2075
plot_diagnostics(proc_data$logCPM, proc_data$vfit$E,
  group_col = proc_data$samples$group
)
#> $density

#> 
#> $RLE

#> 
#> $MDS

#>