variation.within.entities: Variation within entities

In yavorska/AchillesPackage: Achilles Application Functions

Description

Generate a plot comparing the LFC values of each shRNA of a given gene within all entities. The entity scores are calculated based on the mean or median of the relevant cell line scores.

Usage

variation.within.entities(object, geneName, type = "value",
  statistic = "mean", ...)

Arguments

object	An RNAi object.
geneName	A character string giving the name of the gene in question, e.g. "MDM4".
type	The type of values one wishes to show. Either "rank" or "value" (for the LFC scores).
statistic	A statistic used to group the cell line scores, can either be "mean" or "median".
...	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)])

variation.within.entities(object = RNAiObject, geneName = "MDM4", type = "value", statistic = "mean")

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