PlotHotspots: PlotHotspots

Description Usage Arguments Details Value Author(s) Source Examples

Description

PlotHotspots: Plot hot spot for CNVs.

Usage

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PlotHotspots(CNVsDF, Hotspots, ListOfRawDataPath, Cores = 1, Skip = 10,
  Alpha = 1, Times = 10, NumSamples = 20, penalty = 60,
  Quantile = FALSE, QSpline = FALSE, sd = 0.18, OverlapMin = 0.9,
  OverlapMax = 1.1, SNPList = NULL)

Arguments

CNVsDF:

Data frame with CNVs, default = Unknown.

Hotspots:

Unknown, default = Unknown.

ListOfRawDataPath:

Full path for each sample. You can get it using the command: Files <- list.files(path=PathRawData, pattern=Pattern, full.names=TRUE, recursive=recursive). Than use ListOfRawDataPath=Files.

Cores:

The number of cores used, default = 1.

Skip:

Integer, the number of lines of the data file to be skipped before beginning to read the data, default = 10.

Penalty:

The coefficient of the penalty for degrees of freedom, default = 60.

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, Log R Ratio standard deviation for the quantile normalization, default = 0.18.

Details

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

Value

Png files

Author(s)

Marcelo Bertalan, Louise K. Hoeffding.

Source

http://biopsych.dk/iPsychCNV

Examples

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Unknown. 

mbertalan/iPsychCNV documentation built on May 22, 2019, 12:19 p.m.