PlotTabForestBiomarker: Generate forest plot and summarization table for 2-arm or...

In lengning/gClinBiomarker: gClinBiomarker: an R package for clinical biomarker analyses

Description

This function creates a forest plot along with table with summary statistics to infer biomarker effects, within a single arm or across two treatment arms. The outcome could be survival, binary or continuous. This function can be used to summarize a single biomarker variable

Usage

PlotTabForestBiomarker(data, outcome.class = c("survival", "binary"),
  outcome.var, trt = NULL, var = NULL, var.class = NULL,
  var.name = NULL, percentile.cutoff = 0.5, numerical.cutoff = NULL,
  greater = TRUE, less = FALSE, greater.by.less = FALSE,
  across.and.within = FALSE, equal.in.high = TRUE, within.bin = FALSE,
  show.itt = TRUE, show.bep = TRUE, bep = NULL, bep.name = "BEP",
  itt.name = "All", bep.indicator = 1, covariate = NULL, strata = NULL,
  tabforest = FALSE, quantile.type = 2, digits = 2, cutoff.digits = 2,
  placebo.code = NULL, active.code = NULL, rsp.cat = TRUE,
  rsp.response = c("CR", "PR"), rsp.nonresponse = c("SD", "PD", "NON CR/PD",
  "NE", NA), var.code = NULL, surv.conf.type = "plain", ties = "efron",
  alpha = 0.05, main = NULL, main.prefix = NULL, sub = NULL,
  clip = NULL, xticks = NULL, xticks.digits = 1, xlab = NULL,
  cex.headings = 1.1, cex.note = 0.8, cols = NULL, only.stat = FALSE,
  pdf.name = NULL, pdf.param = list(width = 12, height = 4.5),
  par.param = list(cex = 1, cex.main = 1, cex.sub = 1, cex.axis = 1))

Arguments

data	input data frame. Rows are patients and columns are variables (e.g. demographics variables, time to event variables, biomarker variables, treatment indicator, etc.). One patient per row.
outcome.class	type of the outcome variable. Default is c("survival", "binary", "continuous"). Continuous is not available now
outcome.var	name of the outcome varible. If the outcome.class is binary or coutinuous, only one value should be provided. If the outcome.class is survival, two values should be provided - name of the 'time to event' variable and 'censorship' variable For the censoring variable, 1 indicates event and 0 indicates censoring. In all cases but when outcome.class=binary and rsp.cat=TRUE, patients with missing outcome variable (NA) will be excluded from BEP.
trt	name of the treatment variable. If this is NULL, within-arm analysis will be performed
var	name of the biomarker variable. only one variable should be specified.
var.class	class of the variable. valid categories are "numeric", "categorical". If the class is continuous, user needs to specify percentile.cutoff or numerical.cutoff to dichotomize the continuous measure into subgroups
var.name	display name for the biomarker variable
percentile.cutoff	percentile to dichotomize continuous biomarker measure. This could be a vector with multiple elements. Values should be between 0 and 1
numerical.cutoff	raw value to dichotomize continuous biomarker measure. numerical.cutoff and percentile.cutoff cannot be both specified
greater	whether calculate summary statistics within the subgroup whose biomarker value is greater than or equal to cutoff value. If this is TRUE, in 2-arm study, across-arm HR within biomarker high group will be calculated. In single arm study HR of biomarker high vs low will be calculated.
less	whether calculate summary statistics within the subgroup whose biomarker value is less than the cutoff value. greater and less can both be TRUE
greater.by.less	whether show "greater" bin and "less" bin in consecutive rows. Default is FALSE. If it is TRUE, parameters greater and less will be both set as TRUE
across.and.within	whether show across- and within- arm results in the same figure. Default is FALSE. This parameter will be ignored if number of arm is 1. If it is TRUE, within-arm analysis results will be shown below the across-arm results.
equal.in.high	whether include equal in high group. Default is TRUE. If it is TRUE, ">=" and "<" will be applied. Otherwise "<=" and ">" will be applied.
within.bin	whether calculate summary statistics within bin (e.g. > cutoff1 and <= cutoff2). If within.bin is TRUE, greater and less will be set as FALSE.
show.itt	whether calculate summary statistics using all patients in full population (e.g. ITT). This will be ignored in 1arm case
show.bep	whether calculate summary statistics using all patients in BEP (biomarker evaluable population). This will be ignored in 1arm case
bep	name of the column which indicates biomarker evaluable population. If it is null, patients who have non NA records in biomarker variable will be used as BEP.
bep.name	preferred display name of the biomarker evaluable population. If it is NULL, bep will be used.
itt.name	preferred display name of the full population (e.g. ITT). If it is NULL, "All" will be used.
bep.indicator	In the subpopulation column, which value is used to define the biomarker evaluable population.
covariate	a vector specifying the covariate variables to be adjusted in the model. Default is set to NULL, meaning no adjustment.
strata	name of the stratification variables. Default is set to NULL, meaning no stratification.
tabforest	Default is FALSE. If it is FALSE, forest plot will be generated using forestplot::forestplot() function. If it is TRUE, a table will be generated with forest plots incorpriated
quantile.type	an integer between 1 and 9 selecting one of the nine quantile algorithms. See quantile. Default is 2.
cutoff.digits, digits	cutoff.digits:number of digits for rounding when calculating cutoff. will only be used when percentile.cutoff is specified. digits: number of digits for the summary statistics display
placebo.code	name of the control arm of the treatment variable. If you want to specify placebo code using this parameter, both placebo.code and active.code need to be provided.
active.code	of the treatment/experimental arm of the treatment variable. If you want to specify active code using this parameter, both placebo.code and active.code need to be provided.
rsp.cat	whether the response outcome variable is coded as binary (1 as responder and 0 as non-responder), If rsp.cat is TRUE, responder categories and nonresponder categories should be specified in rsp.response and rsp.nonresponse (all values in the outcome column should be included in rsp.response and rsp.nonresponse) . If rsp.cat is FALSE, the response outcome variable should be coded as binary (0/1). At the same time rsp.response and rsp.nonresponse will be ignored.
rsp.response	categories that should be considered as responder.
rsp.nonresponse	categories that should be considered as non responder.
var.code	ordered levels of the biomarker variable. This will be ignored for continuous biomarker. If the biomarker is categorical and this is NULL, biomarker subgroups will be ordered by the order from factor() function
surv.conf.type	confidence interval type. Default is "plain". see conf.type in survfit
ties	Default is "efron". To match internal sas results, use "exact". See parameter "ties" in coxph.
alpha	type I error rate. Default is 0.05.
main, main.prefix	main title (prefix of title) of the forest plot. Default is "Association of biomarker effect within treatment arms".
sub	sub title under the forest plot. Default is NULL.
clip	range of the x-axis of the forest plot. Default is NULL.
xticks, xticks.digits	x axis tick marks for the forest plot
xlab	xlab for forest plot
cex.headings	amount of magnification of headings of the forest plot relative to cex. Default is 1.1.
cex.note	amount of magnification of the note. Default is 1.
cols	Color of the 'effect size' displayed in the forest plot.
only.stat	if it is TRUE, only summary statistics will be generated. No figure will be generated
pdf.name	name of output pdf file. If it's NULL, the plots will be displayed but not saved as pdf. Default is "forestplot::forestplot.pdf".
pdf.param	a list of parameters that define pdf graphics device. See pdf. Default is list(width=6, height=4.5).
par.param	a list of parameters that define graphcial parameters. See par. Default is list(mar=c(4,4,3,2)).

Author(s)

Ning Leng [e-mail], Alexey Pronin [e-mail], and previous team members (see DESCRIPTION)

Examples

data(input)
PlotTabForestBiomarker(data=input,
                      outcome.class=c("survival"),
                      outcome.var=c("PFS","PFS.event"),
                      trt="Arm",
                      var="KRAS.mutant",
                      var.class="categorical")

lengning/gClinBiomarker documentation built on May 9, 2019, 2:55 p.m.