champ.import: Read data from IDAT file.

In YuanTian1991/ChAMPLite: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Description

A Start Function MD

Usage

champ.import(directory = getwd(),
             offset=100,
             arraytype="450K")

Arguments

directory	Location of IDAT files, default is current working directory.(default = getwd())
offset	offset is set to make sure no inf value would be returned.(default = 100)
arraytype	Choose microarray type is "450K" or "EPIC".(default = "450K")

Value

beta	A matrix of beta methylation scores for all probes and all samples (No filtering has been don).
M	A matrix of M methylation scores for all probes and all samples (No filtering has been done).
pd	pd file of all sample information from Sample Sheet, which would be very frequently by following functions as DEFAULT input, thus it's not very necessarily, please don't modify it.
intensity	A matrix of intensity values for all probes and all samples, the information would be used in champ.CNA() function. It has not been filtered. Actually, intensity are the sum of Meth Matrix and UnMeth Matrix.
detP	A matrix of detection p-values for all probes and all samples.
beadcount	A matrix beads for each probe on each sample. Value less then 3 has been set NA.
Meth	Methylated Matrix for all probe and all samples.
UnMeth	UnMethylated Matrix for all probe and all samples.

Author(s)

Yuan Tian

Examples

    ## Not run: 
        myimport <- champ.import(directory=system.file("extdata",package="ChAMPdata"))
    
## End(Not run)

YuanTian1991/ChAMPLite documentation built on Feb. 14, 2022, 6 a.m.