besthr (version 0.3.2)

estimate: Perform bootstrap estimation of confidence intervals of ranked HR scores

Description

estimate carries out estimation of bootstrap confidence intervals on ranked score data. Returns a hrest object of the result Proceeeds by calculating score ranks, then bootstrapping ranks in non-control groups retaining the mean for each bootstrap iteration. Calculates low and high quantiles of bootstrap mean distributions for each group. If technical replicates are provided in a second grouping column these will be averaged before proceeding.

Usage

estimate(df, ..., control = "A", nits = 100, low = 0.025, high = 0.975)

Value

a list object of class "hrest"

Arguments

df

data frame of score and group data. Contains minimally a score and group column

...

bare names of columns to use, minimally the score column and the group column in that order. Optionally a third technical replicate column can be provided

control

the value of the grouping column taken to be the control group

nits

the number of bootstap iterations to be done

low

the low probability value of the quantile

high

the high probability value of the quantile

Examples

 d1 <- make_data()
 estimate(d1, score, group)

 d2 <- make_data2()
 estimate(d2, score_column_name, sample_column_name, rep_column_name )

# \donttest{
 d3 <- make_data3()
 estimate(d3, score, sample, rep, nits = 1000)
# }