Description Usage Arguments Details Value Author(s) Source Examples
Stackplot: Produces stacked plots of CNV calls from multiple samples for a given locus.
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Pos: |
Position of the loci to plot in the form chr21:1050000-1350000. |
IDs: |
List of IDs to plot |
PathRawData: |
The path to the raw data files contining LRR and BAF values to plot. |
CNVs: |
Data frame containing the CNVs called on the samples. |
Highlight: |
Position of a specific region to be highlighted, in the form chr21:1050000-1350000, default = NULL. |
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 with a deidentified ID - requires that the CNV data frame contains a column called ID_deidentified, default = NA. |
OutFolder: |
Path for saving outputfiles. Default is current folder |
Files: |
Full path for each sample. You can get it using the command: Files <- list.files(path=PathRawData, pattern=Pattern, full.names=TRUE, recursive=FALSE). Then use Files=Files. |
Pattern: |
File pattern in the raw data, default = "*". |
Recursive: |
Logical, Should files matching patterns in subfolders be included, default = FALSE. |
For each sample two tracks are plotted representing the Log R Ratio (LRR) and the B Allele Frequency (BAF).
A png plot of the specified loci.
Johan Hilge Thygesen, Ida Elken Sønderby, Louise K. Hoeffding.
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