survivaly_analysis: Survival analysis

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Survival analysis

Description

Survival analysis

Usage

survivaly_analysis(
  Event = NULL,
  Time = NULL,
  Group = NULL,
  group.prefix = NA,
  ylab = "Survival probability",
  title = "",
  palette = "lancet",
  conf.int = FALSE,
  legend.position = "none",
  linetype = 1,
  calculate.pval = FALSE,
  remove.na = FALSE,
  only.consider.group = NULL,
  not.consider.group = NULL,
  risk.table = TRUE,
  best.point = F,
  cut.quantile = NULL,
  cut.label = NULL,
  surv.median.line = "none",
  pval = TRUE,
  returnSurv.fit = FALSE,
  maximum.days = NULL
)

Arguments

Event	Required 0,1
Time	Required
Group	Required
group.prefix	Default ""
title	Default "Suvival analysis"
palette	the color palette to be used.
conf.int	logical value. If TRUE, plots confidence interval.
legend.position	one of c("top", "bottom", "left", "right", "none"). Default is "none".
linetype	line types. Allowed values includes i) "strata" for changing linetypes by strata (i.e. groups); ii) a numeric vector (e.g., c(1, 2)) or a character vector c("solid", "dashed").
calculate.pval	If TRUE, just reture p value data.frame.
remove.na	If remove NA samples
only.consider.group	Groups to consider
not.consider.group	Groups to exclude
risk.table	Default TRUE. Show the strata Table
best.point	If best cut point wanted, pls input values by Group variable
cut.quantile	Love this paramter, handsome
surv.median.line	character vector for drawing a horizontal/vertical line at median survival. Allowed values include one of c("none", "hv", "h", "v"). v: vertical, h:horizontal.
pval	logical value, a numeric or a string or show "HR" or "PHR" or "HRCI" or "PHRCI"
returnSurv.fit	If TRUE, reture the fit object. Easy to check median survival time
maximum.days	The maximum days or months

Examples

data(LIRI)
loonR::survivaly_analysis(LIRI$status, LIRI$time, LIRI$ANLN > mean(LIRI$ANLN), legend.position="right", risk.table = F )
loonR::survivaly_analysis(LIRI$status, LIRI$time, LIRI$ANLN, best.point = T)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.