compSurv: Comparison of prognosis by Kaplan-Meier survival curve
In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description Usage Arguments Value Examples

This function calculates Kaplan-meier estimator and generate survival curves with log-rank test to detect prognostic difference among identified subtypes. If more than 2 subtypes are identified, pair-wise comparisons will be performed with an additional table printed on the survival curve.

compSurv(
  moic.res = NULL,
  surv.info = NULL,
  convt.time = "d",
  surv.cut = NULL,
  xyrs.est = NULL,
  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
    "#023E8A", "#9D4EDD"),
  p.adjust.method = "BH",
  surv.median.line = "none",
  fig.name = NULL,
  fig.path = getwd()
)

`moic.res`	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
`surv.info`	A data.frame with rownames of observations and with at least two columns of 'futime' for survival time and 'fustat' for survival status (0: censoring; 1: event)
`convt.time`	A string value to indicate how to convert the survival time; value of 'd' for days, 'm' for months and 'y' for years; "d" by default.
`surv.cut`	A numeric value to indicate the x-axis cutoff for showing the maximal survival time. NULL by default (show 0-maximum survival time range).
`xyrs.est`	An integer vector to estimate probability of surviving beyond a certain number (x) of years (Estimating x-year survival); NULL by default.
`clust.col`	A string vector storing colors for each subtype.
`p.adjust.method`	A string value for indicating method for adjusting p values (see p.adjust). Allowed values include one of c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none'); "BH" by default.
`surv.median.line`	A string value for drawing a horizontal/vertical line at median survival. Allowed values include one of c('none', 'hv', 'h', 'v'). v: vertical, h:horizontal; "none" by default.
`fig.name`	A string value to indicate the output path for storing the kaplan-meier curve.
`fig.path`	A string value to indicate the name of the kaplan-meier curve.

A figure of multi-omics Kaplan-Meier curve (.pdf) and a list with the following components:

fitd an object returned by survdiff.

fid an object returned by survfit.

xyrs.est x-year probability of survival and the associated lower and upper bounds of the 95

overall.p a nominal p.value calculated by Kaplain-Meier estimator with log-rank test.

pairwise.p an object of class "pairwise.htest" which is a list containing the p values (see pairwise_survdiff); (only returned when more than 2 subtypes are identified).