spkAll: Spike-in Functions Wrapper

In mccallm/spkTools: Methods for Spike-in Arrays

Description

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

Usage

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

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

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