FilterFromCNVs: FilterFromCNVs
In mbertalan/iPsychCNV: iPsychCNV

Description Usage Arguments Details Value Author(s) Source Examples

FilterFromCNVs: Filter CNV from other methods.

1 2	FilterFromCNVs(CNVs, PathRawData, MinNumSNPs = 10, Source = "iPsychCNV", Skip = 0, Cores = 1)

`CNVs:`	Data frame with CNVs.
`PathRawData:`	The path to the raw data files containing Log R Ratio (LRR) and B Allele Frequency (BAF) values. Example: "/media/NeoScreen/NeSc_home/ILMN/iPSYCH/Version2".
`MinNumSNPs:`	Minimum number of SNPs per CNV, default = 10.
`Source:`	Which method is the original call, default = iPsychCNV.
`Skip:`	Integer, the number of rows of the data file that should be skipped before beginning tp read the data. Use if file has comments, default = 0.
`Cores:`	Number of cores to run in parallel, default = 1.

Specifically designed to reduce false positive CNVs and handle noisy data from amplified DNA on phenylketonuria (PKU) cards. The function is a pipeline using many subfunctions.

Data frame with the estimated copy number for each chromosome.

Marcelo Bertalan, Louise K. Hoeffding.

http://biopsych.dk/iPsychCNV

LongRoi <- MakeLongMockSample(Mean=c(-0.6, -0.3, 0.3, 0.6), Size=c(200, 400, 600))
# GADA
Sample <- read.table("LongMockSample.tab", sep="\t", header=TRUE, stringsAsFactors=F)
Gada <- RunGada(Sample)
Gada.filter <- FilterFromCNVs(CNVs=Gada, PathRawData=".", MinNumSNPs=10, Source="Gada", Skip=0, Cores=1)
See iPsychCNV tutorial for more examples
http://biopsych.dk/iPsychCNV/tutorial.html