View source: R/pgxSegprocess.R
pgxSegprocess | R Documentation |
This function extracts segment variants, CNV frequency, and metadata from local "pgxseg" files and supports survival data visualization.
pgxSegprocess(
file,
group_id = "group_id",
show_KM_plot = FALSE,
return_metadata = FALSE,
return_seg = FALSE,
return_frequency = FALSE,
assembly = "hg38",
bin_size = 1e+06,
overlap = 1000,
soft_expansion = 0.1,
...
)
file |
A string specifying the path and name of the "pgxseg" file where the data is to be read. |
group_id |
A string specifying which id is used for grouping in KM plot or CNV frequency calculation. Default is "group_id". |
show_KM_plot |
A logical value determining whether to return the Kaplan-Meier plot based on metadata. Default is FALSE. |
return_metadata |
A logical value determining whether to return metadata. Default is FALSE. |
return_seg |
A logical value determining whether to return segment data. Default is FALSE. |
return_frequency |
A logical value determining whether to return CNV frequency data. The frequency calculation is based on segments in segment data and specified group id in metadata. Default is FALSE. |
assembly |
A string specifying the genome assembly version to apply to CNV frequency calculation and plotting. Allowed options are "hg19" and "hg38". Default is "hg38". |
bin_size |
Size of genomic bins used in CNV frequency calculation to split the genome, in base pairs (bp). Default is 1,000,000. |
overlap |
Numeric value defining the amount of overlap between bins and segments considered as bin-specific CNV, in base pairs (bp). Default is 1,000. |
soft_expansion |
Fraction of |
... |
Other parameters relevant to KM plot. These include |
Segments data, CNV frequency object, meta data or KM plots from local "pgxseg" files
file_path <- system.file("extdata", "example.pgxseg",package = 'pgxRpi')
info <- pgxSegprocess(file=file_path,show_KM_plot = TRUE, return_seg = TRUE, return_metadata = TRUE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.