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

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

Upload of raw HumanMethylation450K or HumanMethylationEPIC data from IDAT files.

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. In new version champ.load() function, we provided a new loading method, which is coded by ChAMP group. User may set "method" parameter as "minfi" to use old minfi way. Note that new "ChAMP" would NOT return rgSet and mset as "minfi" object, only pain matrix or data frame would be returned, which makes it easier to intepret the result, but it also means current ChAMP can not works on "SWAN" and "FunctionNormalization" method in champ.norm(), you can still use "BMIQ" and "PBC" method though.

Usage

champ.load(directory = getwd(),
           method="ChAMP",
           methValue="B",
           autoimpute=TRUE,
           filterDetP=TRUE,
           ProbeCutoff=0,
           SampleCutoff=0.1,
           detPcut=0.01,
           filterBeads=TRUE,
           beadCutoff=0.05,
           filterNoCG=TRUE,
           filterSNPs=TRUE,
           population=NULL,
           filterMultiHit=TRUE,
           filterXY=TRUE,
           force=FALSE,
           arraytype="450K")

Arguments

directory	Location of IDAT files, default is current working directory.(default = getwd())
method	Method to load data, "ChAMP" method is newly provided by ChAMP group, while "minfi" is old minfi way.(default = "ChAMP")
methValue	Indicates whether you prefer m-values M or beta-values B. (default = "B")
autoimpute	If after filtering (or not do filtering) there are NA values in it, should impute.knn(k=3) should be done for the rest NA?
filterDetP	If filter = TRUE, then probes above the detPcut will be filtered out.(default = TRUE)
ProbeCutoff	The NA ratio threshhold for probes. Probes with above proportion of NA will be removed.
SampleCutoff	The failed p value (or NA) threshhold for samples. Samples with above proportion of failed p value (NA) will be removed.
detPcut	The detection p-value threshhold. Probes about this cutoff will be filtered out. (default = 0.01)
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)
force	A parameter in minfi's read.metharray.exp function, if your arrays are not coming from same batch, force parameter would allow you to select their common probes and do analysis on them.(default = FALSE)
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/ChAMP documentation built on Feb. 21, 2023, 4:57 p.m.