Read and summarize gistic output.
A little function to summarize gistic output files. Summarized output is returned as a list of tables.
readGistic( gisticAllLesionsFile = NULL, gisticAmpGenesFile = NULL, gisticDelGenesFile = NULL, gisticScoresFile = NULL, cnLevel = "all", isTCGA = FALSE, verbose = TRUE )
gisticAllLesionsFile |
All Lesions file generated by gistic. e.g; all_lesions.conf_XX.txt, where XX is the confidence level. Required. Default NULL. |
gisticAmpGenesFile |
Amplification Genes file generated by gistic. e.g; amp_genes.conf_XX.txt, where XX is the confidence level. Default NULL. |
gisticDelGenesFile |
Deletion Genes file generated by gistic. e.g; del_genes.conf_XX.txt, where XX is the confidence level. Default NULL. |
gisticScoresFile |
scores.gistic file generated by gistic. |
cnLevel |
level of CN changes to use. Can be 'all', 'deep' or 'shallow'. Default uses all i.e, genes with both 'shallow' or 'deep' CN changes |
isTCGA |
Is the data from TCGA. Default FALSE. |
verbose |
Default TRUE |
Requires output files generated from GISTIC. Gistic documentation can be found here ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm
A list of summarized data.
all.lesions <- system.file("extdata", "all_lesions.conf_99.txt", package = "maftools")
amp.genes <- system.file("extdata", "amp_genes.conf_99.txt", package = "maftools")
del.genes <- system.file("extdata", "del_genes.conf_99.txt", package = "maftools")
scores.gistic <- system.file("extdata", "scores.gistic", package = "maftools")
laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gistic, isTCGA = TRUE)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.