p53.dependency.by.entity: P53 dependency by entity

In yavorska/AchillesPackage: Achilles Application Functions

Description

Generate a plot comparing the dependency of various shRNAs on the mutation status of p53 for the cells lines of a given entity.

Usage

p53.dependency.by.entity(object, entityName, geneName, p53 = "all",
  type = "all", ...)

Arguments

object	An RNAi object.
entityName	A character string giving the name of the entity in question, e.g. "BONE".
geneName	A character string giving the name of the gene in question, e.g. "MDM4".
p53	The types of cell lines to include. Can be "all", "MUT", "WT", or "NA".
type	The style of plot one wishes to show, can be one of "box" or "line".
...	Any other additions to the ggplot. One can change the theme, plot name, etc. as desired.

Value

A ggplot object.

Examples

data("Achilles2.4_Data")
data("Achilles2.4_annotation")

RNAiObject <- new(Class = "RNAi", genes = Achilles2.4_Data$Gene,
                  sequences = Achilles2.4_Data$Name,
                  cancers = colnames(Achilles2.4_Data)[-(1:2)],
                  cancersP53 = Achilles2.4_annotation,
                  values = Achilles2.4_Data[,-(1:2)])

p53.dependency.by.entity(object = RNAiObject, entityName = "Lung", geneName = "MDM4", p53 = "all", type = "line")

yavorska/AchillesPackage documentation built on May 4, 2019, 2:31 p.m.