Description Usage Arguments Details Value Author(s) Source Examples
PlotCNVsFromDataFrame: Function to plot Log R Ratio (LRR) and B Allele Frequency (BAF) of CNVs from a data frame (DF).
1 2 3 4 |
DF: |
Data frame with predicted CNVs for each sample, default = Unknown. |
PathRawData: |
The path to the raw data files containing LRR and BAF values. |
Cores: |
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 = 0. |
PlotPosition: |
Unknown, default = 1. |
Pattern: |
File pattern in the raw data, default = "*". |
Recursive: |
Logical, Unknown, default = TRUE. |
Dpi: |
Dots per inch, default = 300. |
Files: |
Unknown, default = NA. |
SNPList: |
Getting chromosome (Chr) and position from another source than the RawFile - input should be the full path of the SNPList with columns: Name, Chr, and 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, default = NULL. |
Key: |
Exchange the ID printed on the plot and in the name of file with a deidentified ID - requires that the DF contains a column called ID_deidentified, default = NA. |
XAxisDefine: |
Position of a specific region to be plotted, in the form chr21:1050000-1350000, default = NULL. |
OutFolder: |
Path for saving outputfiles, default is the current folder. |
Specifically designed to handle noisy data from amplified DNA on phenylketonuria (PKU) cards. The function is a pipeline using many subfunctions.
One BAF- and LRR-plot for each CNV.
Marcelo Bertalan, Ida Elken Sønderby, Louise K. Hoeffding.
1 2 3 4 5 | # Creating CNVs from MockData & plotting
MockCNVs <- MockData(N=2, Type="Blood", Cores=10)
CNVs <- iPsychCNV(PathRawData=".", Pattern="^MockSample*", Skip=0)
CNVs.Good <- subset(CNVs, CN != 2) # keep only CNVs with CN = 0, 1, 3, 4.
PlotCNVsFromDataFrame(DF=CNVs.Good[1,], PathRawData=".", Cores=1, Skip=0, Pattern="^MockSamples*", key=NA, OutFolder="../", XAxisDefine = NULL)
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