dbStats: dbStats builds dataset for a given betas matrix composed of...

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

dbStats builds dataset for a given betas matrix composed of engineered features from the given database sets

Description

dbStats builds dataset for a given betas matrix composed of engineered features from the given database sets

Usage

dbStats(
  betas,
  databases,
  fun = mean,
  na.rm = TRUE,
  n_min = NULL,
  f_min = 0.1,
  long = FALSE
)

Arguments

betas	matrix of beta values where probes are on the rows and samples are on the columns
databases	List of vectors corresponding to probe locations for which the features will be extracted
fun	aggregation function, default to mean
na.rm	whether to remove NA
n_min	min number of non-NA for aggregation function to apply, overrides f_min
f_min	min fraction of non-NA for aggregation function to apply
long	produce long-form result

Value

matrix with samples on the rows and database set on the columns

Examples

library(SummarizedExperiment)
se <- sesameDataGet('MM285.467.SE.tissue20Kprobes')
head(dbStats(assay(se), "MM285.chromHMM")[,1:3])
sesameDataGet_resetEnv()

zwdzwd/sesame documentation built on April 28, 2024, 12:48 p.m.