Description Usage Arguments Value
View source: R/detGeneStatuses.R
Determine gene amplifications and biallelic losses
1 2 3 4 5 6 7 8 9 10 11 | detGeneStatuses(
out.dir,
input.file.paths = c(germ_vcf = "", som_vcf = "", gene_cnv = "", cnv = ""),
sample.name,
bed.file = BED_FILE,
java.path = JAVA_PATH,
snpsift.path = SNPSIFT_PATH,
chrom.arm.split.method = "hmf",
do.snpeff.ann = F,
verbose = T
)
|
out.dir |
Path to output dir |
input.file.paths |
A list or vector supplying the path output files from the HMF pipeline. |
sample.name |
Name of the sample This list should be in the form c(germ_vcf=”, som_vcf=”, gene_cnv=”, cnv=”) |
bed.file |
Path to the bed file containing the genes of interest. This bed file should also contain the column ensembl_gene_id |
java.path |
Path the the java binary |
snpsift.path |
Path to the SnpSift jar |
chrom.arm.split.method |
Can be 'hmf' or 'gap'. Refer to documentation for calcChromArmPloidies(). |
do.snpeff.ann |
Annotate SNV/indels variant type with snpeff? |
verbose |
Show progress messages? |
Writes a diplotypes table to the output dir
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