appendCdfEnvAffy: append probe sets to a CdfEnvAffy

In altcdfenvs: alternative CDF environments (aka probeset mappings)

Description

append probe sets to a CdfEnvAffy

Usage

appendCdfEnvAffy(acdfenv, id, i, nocopy = TRUE)

Arguments

acdfenv	instance of class CdfEnvAffy
id	identifier for the probe set to add
i	a matrix of indexes (see details)
nocopy	whether to make a copy of the environment or not (see details)

Details

The matrix i must have one column per probe type. For typical Affymetrix chip types, there are two probe types: "pm" and "mm".

nocopy set to TRUE means that the environment is added the probe set 'in-situ' (this can boost execution speed if you add a lot of probe sets).

Value

An CdfEnvAffy is returned

Examples

data(cdfenvEx)

## pm and mm probe set
m <- matrix(1:10, ncol = 2)
colnames(m) <- c("pm", "mm")

appendCdfEnvAffy(cdfenvEx, "blabla", m)

indexProbes(cdfenvEx, c("pm", "mm"), "blabla")

## pm only probe set
m <- matrix(6:9, ncol = 1)
colnames(m) <- c("pm")
appendCdfEnvAffy(cdfenvEx, "blabla2", m)
## note that the unspecified "mm" were set to NA
indexProbes(cdfenvEx, c("pm", "mm"), "blabla2")

altcdfenvs documentation built on Nov. 8, 2020, 7:12 p.m.