terms.to.keep: Filtering Function to Identify which Proteins are retained

In pranavdorbala/proteomicsHF: ARIC Proteomics of Heart Failure -- Biomarker Discovery Pipeline

Description

This function calculates which proteins are retained at specified significance intervals. For example, when the univariate results are provided, this function returns all proteins that are bonferroni significant.

Usage

## S3 method for class 'to.keep'
terms(data, .pval, .src, .terms = NULL)

Arguments

data	The Univariate (and Validation) Tibble with Regression Results. Output of cox.arry().
.pval	The significance level to examine which proteins are retained.
.src	The tibble in which we examine retained proteins. .src = 1 means the Derivation dataset if the derivation and validation sets are row-bound.
.terms	Vector of terms to limit examination of significance to. Not necessary to be specified.

Details

This function can also be used to check which proteins are retained in validation.

Value

kept

A vector containing all Proteins that were retained by the filter

data

A Tibble with the Hazard Ratio and Significance of Retained Proteins

Examples

## Not run: 
plot.data <-
  dplyr::bind_rows(univariate.results,
                   validation.results) %>%
  dplyr::mutate(Name = labels[term, "name"])

bonferroni <-
  terms.to.keep(plot.data,
                .pval = 0.05/length(proteins), 1)
falsediscr <-
  terms.to.keep(plot.data,
                .pval = 0.05, 1)

retained <-
  terms.to.keep(plot.data,
                .pval = 0.05, 2,
                .terms = bonferroni$kept)


## End(Not run)

pranavdorbala/proteomicsHF documentation built on March 9, 2021, 12:22 a.m.