plot_QC_repl_var: Replicates variation plot

In Rundmus/BAf-R_package: Binder Array data hanlding package in facility

Description

Draw the plot that shows the distribution of variation statistics (e.g. coefficient of variation(CV)) of replicates

Usage

plot_QC_repl_var(
  baf,
  i_repl = 1:nrow(baf),
  by_s = batch_colname(baf, "sample"),
  varFUN = function(x) {     sd(x, na.rm = T)/mean(x, na.rm = T) },
  col_lines = palette(),
  main = deparse(substitute(baf)),
  xlab = "Coef. of var.",
  ylab = "Density",
  xlim = c(0, 0.5),
  ylim = NULL,
  lty = c("solid", "dashed"),
  lwd = c(2, 1),
  ...
)

Arguments

baf	an object of the BAf-class
i_repl	an integer or logical index vector of the rows that have replicated samples
by_s	by which the samples are grouped. The varFUN is applied to each group and the results are combined. This should be given by a character string of a column name in @sinfo.
varFUN	a function to compute a variation statistics. The default is the function to compute the coefficienct of variation.
col_lines	a named vector of line colors in character strings
main, xlab, ylab, xlim, ylim	same as those for plot
lty, lwd	the first value is for the line to show the variation of replicates, while the second is for the other samples. Individual values are same those for plot
...	the arguments passed over to plot and lines

Value

a list that contains computed varaition statistics of the replicates and all the other samples

Author(s)

Mun-Gwan Hong <[e-mail]>

Examples

data(sba)
sba2 <- sba[sba@sinfo$cohort != "EMPTY", ]
plot_QC_repl_var(sba2, sba2@sinfo$cohort == "MIX_1")

Rundmus/BAf-R_package documentation built on May 18, 2020, 12:59 p.m.