MMRFVariant_SurvivalKM: MMRFVariant_SurvivalKM

In marziasettino/MMRFVariant: R package for variant analysis from MMRF-CoMMpass data source

MMRFVariant_SurvivalKM

Description

Creates a KM survival plot from MMRF-RG patient clinical data using survival library. It uses the fields D_PT_deathdy, D_PT_PRIMARYREASON and D_PT_lstalive columns for groups.

Usage

MMRFVariant_SurvivalKM(
  patient,
  trt,
  variant.ann,
  list.variant,
  FilterBy = "treatment",
  legend = "Legend",
  labels = NULL,
  xlim = NULL,
  main = "Kaplan-Meier Survival Curve",
  ylab = "Probability of survival",
  xlab = "Time since diagnosis (days)",
  filename = "survival.pdf",
  color = NULL,
  height = 8,
  width = 12,
  dpi = 300,
  pvalue = TRUE,
  conf.range = TRUE
)

Arguments

patient	is the data.frame of the patient clinical data downloaded from MMRF-Commpass Researcher Gateway (i.e. MMRF_CoMMpass_IA15_PER_PATIENT file) and imported into environment.
trt	is the data.frame of the patient clinical data (i.e. treatment-response) downloaded from MMRF-Commpass Researcher Gateway (i.e. MMRF_CoMMpass_IA15_STAND_ALONE_TRTRESP file) and imported into environment.
variant.ann	is the data.frame of the annotated variants downloaded from MMRF-Commpass Researcher Gateway (i.e. MMRF_CoMMpass_IA15a_All_Canonical_Variants file) and imported into environment.
FilterBy	Column with groups to plot. This is a mandatory field. Example: Ethnicity Ethnicity Stage ISS Stage Treatment Treatment class Bestresp Best overall response Gender gender Effect effect Biotype biotype
legend	Legend title of the figure
labels	labels of the plot
xlim	x axis limits e.g. xlim = c(0, 1000). Present narrower X axis, but not affect survival estimates.
main	main title of the plot
ylab	y axis text of the plot
xlab	x axis text of the plot
filename	The name of the pdf file.
color	Define the colors/Pallete for lines.
height	Image height
width	Image width
dpi	Figure quality
pvalue	show p-value of log-rank test
conf.range	show confidence intervals for point estimates of survival curves.
Listvariant	is the list of the variants to analyze.
expand	show or not an expanded plot

Value

Survival plot

Examples

patient <- data.frame(public_id=c("MMRF_0000","MMRF_0001",
                                   "MMRF_0002","MMRF_0003",
                                   "MMRF_0004","MMRF_0005",
                                   "MMRF_0006","MMRF_0007",
                                   "MMRF_0008","MMRF_0009"),
                      D_PT_PRIMARYREASON = c("Death",NA,NA,"Death","Death", 
                                             "Death","NA","NA","Death","Death"),
                      D_PT_deathdy =  c(NA,NA,2226,172,NA,NA,1328,681,786,NA),
                      D_PT_lstalive = c(250,356,NA,NA,1814,223,NA,NA,NA,1450),
                      DEMOG_GENDER = c(rep(1,5),rep(2,5)), #2 stands for female, 1 standas for male#'                       
                      DEMOG_ETHNICITY=c(rep("Hispanic or Latino",5),rep("Not Hispanic or Latino",5)),
                      D_PT_issstage_char=c(rep("Stage III",3),rep("Stage II",2),rep("Stage I",5))
 )


trt<- data.frame(public_id=c("MMRF_0000","MMRF_0001",
                              "MMRF_0002","MMRF_0003",
                              "MMRF_0004","MMRF_0005",
                              "MMRF_0006","MMRF_0007",
                              "MMRF_0008","MMRF_0009"),
                 trtclass=c(rep("Bortezomib-based",2),rep("IMIDs-based",5),rep("combined bortezomib/IMIDs-based",3)),                                                    
                 bestresp=c(rep("Partial Responsed",5),rep("Very Good Partial Response",5))               
                                   
 )



         surv1<-MMRFVariant_SurvivalKM(patient,  

marziasettino/MMRFVariant documentation built on March 28, 2023, 3:16 p.m.