ccfAUC {MesKit} | R Documentation |
The tumor heterogeneity was estimated as the area under the curve (AUC) of the cumulative density function from all cancer cell fractions per tumor
ccfAUC( maf, patient.id = NULL, min.ccf = 0, withinTumor = FALSE, plot.density = TRUE, use.tumorSampleLabel = FALSE, ... )
maf |
A Maf or MafList object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included. |
min.ccf |
The minimum value of CCF. Default 0. |
withinTumor |
Calculate between-region heterogeneity within tumor. Default FALSE. |
plot.density |
Whether to show the density plot. Default TRUE. |
use.tumorSampleLabel |
Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'. |
... |
Other options passed to |
A list containing AUC of CCF and a graph
Charoentong P, Finotello F, et al. Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. Cell reports 2017, 18:248-262.
maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit") clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit") ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit") maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19") ccfAUC(maf)