iPsychCNV: iPsychCNV
In mbertalan/iPsychCNV: iPsychCNV

Description Usage Arguments Details Value Author(s) Source Examples

iPsychCNV: Find Copy Number Variation (CNV) from SNP genotyping arrays.

iPsychCNV(PathRawData = "/media/NeoScreen/NeSc_home/ILMN/iPSYCH/",
  MINNumSNPs = 20, Cores = 1, hg = "hg19", NumFiles = "All",
  Pattern = "22q11_*", MinLength = 10, SelectedFiles = NA, Skip = 10,
  LCR = FALSE, PFB = NULL, chr = NA, penalty = 60, Quantile = FALSE,
  QSpline = FALSE, sd = 0.18, recursive = FALSE, CPTmethod = "meanvar",
  CNVSignal = 0.1, penvalue = 16, OutputPath = NA,
  OutputFileName = "Test", OnlyCNVs = TRUE, SNPList = NULL)

`LCR`	list: Low copy repeat region, list of SNPs that should be removed.
`PFB`	vector: Population frequency 0 to 1 for each SNP in the array.
`PathRawData:`	The path to the raw data files contining Log R Ratio (LRR) and B Allele Frequency (BAF) values.
`MINNumSNPs:`	Minimum number of SNPs per CNV, default = 20.
`Cores:`	Number of cores used, default = 1.
`Hg:`	Human genome version, default = hg19.
`NumFiles:`	Number of files to be analyzed from PathRawData.
`Pattern:`	File pattern in the PathRawData. Example: "*.txt".
`MinLength:`	Minimum CNV length, default = Unknown.
`SelectedFiles:`	List of file names that should be analyzed from PathRawData.
`Skip:`	Integer, the number of lines of the data file to skip before beginning to read data.
`Chr:`	Character, select a specific chromosome to be analyzed.
`Penalty:`	The coefficient of the penalty for degrees of freedom in the GCV criterion. From smooth.spline stats.
`Quantile:`	Logical, if quantile normalization should be applied or not, default = FALSE.
`QSpline:`	Logical, if a cubic smoothing spline should be used to normalize the data, default = FALSE.
`Sd:`	Numeric, LRR standard deviation for the quantile nomarlization, default = 0.18.
`Recursive:`	Logical, should the listing recurse into directories? From list.files base.
`CPTmethod:`	Character, method to find change points from changepoint package by Rebecca Killick. Default "meanvar", or "mean".
`CNVSignal:`	Numeric, minumum CNV signal to be consider a CNV in absolute value, default = 0.1, any CNV with mean LRR in the CNV region with abs(X) < 0.1 is ignored.
`Penvalue:`	Same as pen.value from function cpt.mean at changepoint R package by Rebecca Killick, default = 10. "The theoretical type I error e.g.0.05 when using the Asymptotic penalty. A vector of length 2 (min,max) if using the CROPS penalty. The value of the penalty when using the Manual penalty option - this can be a numeric value or text giving the formula to use. Available variables are, n=length of original data, null=null likelihood, alt=alternative likelihood, tau=proposed changepoint, diffparam=difference in number of alternatve and null parameters".
`OutputPath:`	Character, path for output.
`OutputFileName:`	Character, output file name.
`OnlyCNVs:`	Logical, if TRUE only CNVs with copy number state 0,1,3,4 will be returned. If FALSE will return also changepoint regions with CN = 2.
`SNPList:`	Getting Chr. and Position from another source than the RawFile - input should be the full path of the SNPList with columns: Name, Chr, amd Position. Any positions from the RawFile will be erased. A PFB-column is also allowed but will be overwritten by the PFB-parameter or exchanged with 0.5