champ.load: Upload of raw HumanMethylation450K or HumanMethylationEPIC...

In JoshuaTian/MyChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Description

Function that loads data from IDAT files to calculate intensity. Some kinds of filtering will be conducted as well such as unqualied CpGs, SNP, multihit sites, and XY chromosomes related CpGs.

Usage

champ.load(directory = getwd(),
           methValue="B",
           filterDetP=TRUE,
           detSamplecut=0.1,
           detPcut=0.01,
           removeDetP = 0,
           filterBeads=TRUE,
           beadCutoff=0.05,
           filterNoCG=TRUE,
           filterSNPs=TRUE,
           population=NULL,
           filterMultiHit=TRUE,
           filterXY=TRUE,
           arraytype="450K")

Arguments

directory	Location of IDAT files, default is current working directory.(default = getwd())
methValue	Indicates whether you prefer m-values M or beta-values B. (default = "B")
filterDetP	If filter = TRUE, then probes above the detPcut will be filtered out.(default = TRUE)
detSamplecut	The detection p value threshhold for samples. Samples with above proportion of failed p value will be removed.
detPcut	The detection p-value threshhold. Probes about this cutoff will be filtered out. (default = 0.01)
removeDetP	The removeDetP parameter represents the fraction of samples that can contain a detection p-value above the detPcut.(default = 0)
filterBeads	If filterBeads=TRUE, probes with a beadcount less than 3 will be removed depending on the beadCutoff value.(default = TRUE)
beadCutoff	The beadCutoff represents the fraction of samples that must have a beadcount less than 3 before the probe is removed.(default = 0.05)
filterNoCG	If filterNoCG=TRUE, non-cg probes are removed.(default = TRUE)
filterSNPs	If filterSNPs=TRUE, probes in which the probed CpG falls near a SNP as defined in Nordlund et al are removed.(default = TRUE)
population	If you want to do filtering on specifical populations you may assign this parameter as one of "AFR","EAS"... The full list of population is in http://www.internationalgenome.org/category/population/. (default = TRUE)
filterMultiHit	If filterMultiHit=TRUE, probes in which the probe aligns to multiple locations with bwa as defined in Nordlund et al are removed.(default = TRUE)
filterXY	If filterXY=TRUE, probes from X and Y chromosomes are removed.(default = TRUE)
arraytype	Choose microarray type is "450K" or "EPIC".(default = "450K")

Value

mset	mset object from minfi package, with filtering CpGs discarded.
rgSet	rgset object from minfi package function read.metharray.exp(), contains all information of a .idat methylation dataset. If you want to do more analysis than functions provided by ChAMP, you can take this as a start point.
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. CpGs has been filtered as well.
beta	A matrix of methylation scores (M or beta values) for all probes and all samples.
detP	A matrix of detection p-values for all probes and all samples.

Author(s)

Yuan Tian

References

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD and Irizarry RA (2014). Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays. Bioinformatics, 30(10), pp. 1363-1369. doi: 10.1093/bioinformatics/btu049.

Jean-Philippe Fortin, Timothy Triche, Kasper Hansen. Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array. bioRxiv 065490; doi: https://doi.org/10.1101/065490

Zhou W, Laird PW and Shen H: Comprehensive characterization, annotation and innovative use of Infinium DNA Methylation BeadChip probes. Nucleic Acids Research 2016

Examples

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

JoshuaTian/MyChAMP documentation built on May 7, 2019, 12:04 p.m.