lmTestContrast: lmTestContrast

In soderling-lab/tidyProt: tidy statistical analysis of protein mass spectrometry

Description

assess a contrast for a given linear model as fit by lm

Usage

lmTestContrast(fm, LT, s2_prior = 0, df_prior = 0)

Arguments

fm	fit linear model
s2_prior	prior sigma squared for moderated comparison; see also sigma.
df_prior	prior degrees of freedom for moderated comparison; see also limma::squeezeVar to compute prior degrees of freedom.
contrast	a vector indicating a contrast between model coefficients. See the getContrast function to create a contrast.

Value

a data.frame containing the result for the comparison and the following columns:

Contrast - indicates the comparison between model coefficients.

log2FC - the fold change estimated from the fit model.

percentControl - the fold-change converted to a percent relative to the control (positive) coefficient.

SE - the standard error of the comparison computed as the square root of the variance.

Tstatistic - the t-statistic for the comparison, calculated using equation (11) from Kuznetsova et al., 2017.

Pvalue - the p-value for the comparison, calculated from the t-value and degrees of freedom using the student's t-distribution, pt.

DF - the degrees of freedom for the comparison.

S2 - sigma squared – the estimated standard deviation of the errors or residual standard deviation (sigma) squared – see also ?sigma.

soderling-lab/tidyProt documentation built on Dec. 23, 2021, 3:31 a.m.