CellCycleView {MAGeCKFlute}R Documentation

Estimate cell cycle time for all samples compared to control sample and view.

Description

Estimate cell cycle time in different samples by linear fitting of beta scores, and plot fitting lines, in which x-axis is control beta score and y-axis is beta score of all samples.

Usage

CellCycleView(beta, ctrlname, treatname, main = NULL, filename = NULL,
  width = 5, height = 4, ...)

Arguments

beta

Data frame, which has columns of ctrlname and other samples.

ctrlname

A character, specifying the names of control samples.

treatname

A character, specifying the name of treatment samples.

main

As in 'plot'.

filename

Figure file name to create on disk. Default filename="NULL", which means no output.

width

As in ggsave.

height

As in ggsave.

...

Other available parameters in ggsave.

Value

An object created by ggplot, which can be assigned and further customized.

Author(s)

Wubing Zhang

Examples

data(MLE_Data)
# Read beta score from gene summary table in MAGeCK MLE results
dd = ReadBeta(MLE_Data, organism="hsa")
CellCycleView(dd, ctrlname = c("D7_R1", "D7_R2"), treatname = c("PLX7_R1", "PLX7_R2"))


[Package MAGeCKFlute version 1.0.1 Index]