Description Usage Arguments Details Value Author(s) Source Examples
PlotHotspots: Plot hot spot for CNVs.
1 2 3 4 | 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)
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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. |
Specifically designed to handle noisy data from amplified DNA on phenylketonuria (PKU) cards. The function is a pipeline using many subfunctions.
Png files
Marcelo Bertalan, Louise K. Hoeffding.
1 | Unknown.
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