panoply: Personalized Cancer Report

Description Usage Arguments Details Value

Create Circos Plot of copy number, RNA expression events, germline and somatic variants. By default, plots DNA mutation (variant/cna) and RNA expression events and shows connections between events in top pathways with a driver gene event. Allows either germline/somatic variants, cna, or all three.

panCircos(panGene, panDrug, caseids, variant = NULL, 
    cna = NULL, gcount, gcinfo, tumorpct = 0.5, 
    tailPct = 0.05, tailEnd = "upper", minTargets = 1, minPathPct = 0.05, 
    minPathSize = 8, minPathways = 1, ...)

`panGene`	A data.frame of drug test results from panGeneSets
`panDrug`	A data.frame of results from panDrugSets
`caseids`	identifiers of subjects that will match to variant column PatientID, and column name of cna and gcount.
`variant`	data.frame for somatic and/or germline variants. Must contain columns CHROM, POS, Gene.Symbol, SampleType (Germline, Tumor) and PatientID that must match the caseid and controlid
`cna`	data.frame with log2 of copy number aberrations. Required columns CHROM, START, STOP, Gene.Symbol, and columns named to match caseid and controlid
`gcount`	Normalized gene expression counts for patients (columns) at gene symbols (rows). Gene symbols are the row names and should match dataset gcinfoPan gene symbols.
`tumorpct`	Vector of approximate tumor percentage for each patient samples given in the order they appear in cases and controls. If a single value is passed, it is used for all patients. Copy number mutation events are called based on their approximate tumor percentage, transformed to the log2-ratio copy number call.
`tailPct`	percentile used to define the most extreme RNA expression events as cancer events per patient; only used when eventOnly=TRUE. Values 0 < tailPct < .5 allowed.
`tailEnd`	perform differential expression tests that are one-sided ("upper" or "lower"), or two-sided ("both"). Also used with tailPct to include both, upper, or lower expression events to be used as cancer events.
`minTargets`	Retain drug results for drugs that target at least minTargets genes in the cancer and network genes.
`minPathPct`	Of reactome pathways affected by gene networks targeted by the drug, only count those with total druggable by the drug in the pathway divided by the total pathway size >= minPathPct.
`minPathSize`	Of reactome pathways affected by gene networks targeted by the drug, only count the pathways that have total genes >= minPathSize.
`minPathways`	Filter drug results to those that target genes in at least minPathways, after accounting for minPathPct and minPathSize.

circos plot of the driver gene events in outer bands, and gene expression events in the inner bands, colored blue if they are over- or under-expressed, and if one of the key drugs target them. Across the center circle, we show genes that are connected as the top cancer drivers connected to their druggable in-network genes.

Nothing is returned

sinnweja/panoply documentation built on Aug. 9, 2019, 9:56 a.m.