optimalPSIcutoff: Calculate optimal alternative splicing quantification cutoff...

Description Usage Arguments Details Value Examples

View source: R/analysis.R

Description

Calculate optimal alternative splicing quantification cutoff to separate survival curves

Usage

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optimalPSIcutoff(clinical, psi, censoring, event, timeStart, timeStop = NULL,
  followup = "days_to_last_followup", session = NULL, filter = TRUE,
  survTime = NULL)

Arguments

clinical

Data frame: clinical data

psi

Numeric: PSI values to test against the cutoff

censoring

Character: censor using "left", "right", "interval" or "interval2"

event

Character: name of column containing time of the event of interest

timeStart

Character: name of column containing starting time of the interval or follow up time

timeStop

Character: name of column containing ending time of the interval

followup

Character: name of column containing follow up time

session

Shiny session (only used for the visual interface)

filter

Boolean or numeric: elements to use (all by default)

survTime

survTime object: times to follow up, time start, time stop and event (optional)

Details

timeStop is only considered if censoring is either interval or interval2

Value

Optimal alternative splicing quantification cutoff

Examples

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clinical <- read.table(text = "2549   NA ii  female
                                840   NA i   female
                                 NA 1204 iv    male
                                 NA  383 iv  female
                               1293   NA iii   male
                                 NA 1355 ii    male")
names(clinical) <- c("patient.days_to_last_followup", 
                     "patient.days_to_death",
                     "patient.stage_event.pathologic_stage",
                     "patient.gender")
timeStart  <- "days_to_death"
event      <- "days_to_death"

psi <- c(0.1, 0.2, 0.9, 1, 0.2, 0.6)
opt <- optimalPSIcutoff(clinical, psi, "right", event, timeStart)

nuno-agostinho/psichomics documentation built on Nov. 1, 2017, 3:18 p.m.