Upload of raw HumanMethylation450K or HumanMethylationEPIC data from IDAT files.

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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

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champ.load(directory = getwd(),
           methValue="B",
           filterDetP=TRUE,
           detPcut=0.01,
           removeDetP = 0,
           filterBeads=TRUE,
           beadCutoff=0.05,
           filterNoCG=TRUE,
           filterSNPs=TRUE,
           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)

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)

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

Examples

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

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