make_fcs: Generic function to construct confidence intervals.

In hemoshear/assayr2: Tools for analyzing assay data

Description

Perform hypothesis test via glht::multcomp() and construct a data.frame with summary values.

Usage

make_fcs(mod, level = 0.95, sig_figs = 2, restore = TRUE,
  pretty = TRUE)

Arguments

mod	A model object of class lm or lmer/lmerTest.
level	A numeric value between 0 and 1 for confidence level. Default is .95.
sig_figs	A numeric value specifying the number of decimal places in percent change columns in result.
restore	Boolean, shold fold-change confidence interval values be transformed into linear space.
pretty	Boolean, should the labels for pvalues lower < .001, be adjusted to "p < .001" to avoid scienctific notation.

Value

A data.frame with:

• fold-change confidence interval (fc_est, fc_lwr, fc_upr)

• the contrast used in glht::multcomp (group - baseline)

• log2_fc (from baseline)

• pct_change (from baseline)

• p-value (adjusted for multiple comparrisons)

• label (pre-formatted with pct_change and p-value for easy plotting)

Examples

data(iris)
mod <- lm(Sepal.Length ~ 0 + Species, data = iris) # use model with intercept set to 0
fc <- make_fcs(mod)

hemoshear/assayr2 documentation built on Nov. 8, 2019, 6:13 p.m.