synlet (version 1.2.2)

siRNAPlot: Plot siRNA data and quality metrics.

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"))