siRNAPlot: Plot siRNA data and quality metrics.

In synlet: Hits Selection for Synthetic Lethal RNAi Screen Data

Description

Plot the normalized RNAi screen data, row data, control signals and Z' factor.

Usage

siRNAPlot(gene, dat, controlsiRNA, FILEPATH = ".", colour = rainbow(10),
  zPrimeMed, zPrimeMean, treatment, control, normMethod = c("PLATE"),
  width = 15, height = 14)

Arguments

gene	gene symbol, case sensitive
dat	synthetic lethal RNAi screen data
controlsiRNA	controlsiRNA could be a vector of several siRNA, including postive/negative control
FILEPATH	path to store the figure
colour	colour used in graphs
zPrimeMed	zPrime factor basing on median
zPrimeMean,	zPrime factor basing on mean
treatment	the treatment condition in EXPERIMENT_MODIFICATION
control	the control condition in EXPERIMENT_MODIFICATION
normMethod	could be a PLATE and negative controls
width	width of the plot
height	height of the plot

Value

Return the ggplot2 objects in a list, which could be plotted individually.

Examples

zF_mean <- zFactor(exampleDat, negativeCon = "scrambled control si1",
  positiveCon = "PLK1 si1")
zF_med <- zFactor(exampleDat, negativeCon = "scrambled control si1",
  positiveCon = "PLK1 si1", useMean = FALSE)
tem.1 <- siRNAPlot("AAK1", exampleDat,
  controlsiRNA = c("lipid only", "scrambled control si1"),
  FILEPATH = ".",  zPrimeMed = zF_med, zPrimeMean = zF_mean,
  treatment = "treatment", control = "control",
  normMethod = c("PLATE", "lipid only", "scrambled control si1"))

synlet documentation built on Nov. 8, 2020, 6:48 p.m.