champ.filter: Do filtering on beta or M matrix. So that user who have no...

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

Description

Function provided a series of filtering on oone solo beta matrix, which contained most filtering on champ.load(). For user may have no IDAT file but only beta matrix or detected P matrix, they can use this function to do filtering, then do analysis.

Usage

champ.filter(beta,
             detP=NULL,
             pd,
             filterDetP=TRUE,
             detSamplecut=0.1,
             detPcut=0.01,
             removeDetP = 0,
             filterNoCG=TRUE,
             filterSNPs=TRUE,
             population=NULL,
             filterMultiHit=TRUE,
             filterXY=TRUE,
             arraytype="450K")

Arguments

beta	One single beta matrix to do filtering, this matrix can be beta matrix or M value matrix.
detP	Detected P value matrix for corresponding beta matrix, it MUST be 100% corresponding, which can be ignored if you don't have.(default = NULL)
pd	pd file related to this beta matrix, must be provided, because maybe filtering would be on pd file.
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)
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

beta	Filtered matrix of methylation scores (M or beta values) for all probes and all samples.
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.

Author(s)

Yuan Tian

References

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"),
                             filterDetP=F,
                             filterBeads=F,
                             filterSNPs=F,
                             filterXY=F,
                             filterNoCG=F,
                             filterMultiHit=F)
        myfilter <- champ.filter(myLoad$beta,myLoad$detP,myLoad$pd)
    
## End(Not run)

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