spkAll: Spike-in Functions Wrapper

Description Usage Arguments Value Author(s) Examples

View source: R/spkAll.R

Description

A wrapper for the functions contained in the spkTools package, which calls each function.

Usage

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spkAll(object, label, model=expr~spike+probe+array, fc=NULL, tol=3,
xrngs=NULL, yrngs=NULL, cuts=c(.6,.99), potQuantile=.995,
gnn=c(25,100,10000), pch=".", output="eps")

Arguments

object

a SpikeInExpressionSet object

label

a character string to insert into the graphs and tables produced

model

model to be passed to spkAnova

fc

the fold change for which fold change plots will be produced

tol

the number of digits after the decimal point in fc

xrngs

ranges for the x-axis of each plot. d=density, s=slope, v=box, m=M vs A

yrngs

ranges for the y-axis of each plot. d=density, s=slope, v=box, m=M vs A

cuts

quantiles used to make the low, medium, and high bins

potQuantile

the desired quantile to compute the probability of being above

gnn

a vector of 3 numbers passed to spkGNN: the desired number of true positives, the number of truly expressed genes, and the number of truly unexpressed genes

pch

plotting point to be used in spkSlope

output

the format in which to save the plots produced. Options are "pdf" and "eps"

Value

The full complement of plots and tables described in the vignette are created and saved in the current working directory.

Author(s)

Matthew N. McCall

Examples

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data(affy)
spkAll(affy, label="affy", fc=2)

mccallm/spkTools documentation built on May 7, 2019, 1:26 p.m.