In martijnvanattekum/cleanse: Tidyverse functions for SummarizedExperiment

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

The SummarizedExperiment's native col- and rowdata accessor functions (colData and rowData) have a number of non-tidyverse compliances:

• They return or require a DFrame object instead of a tibble
• When setting col-/rowdata they cannot be easily used in a pipe

cleanse offers pipe-friendly accessor functions that work with tibbles

library(cleanse)

data(seq_se)
# Get the coldata as a tibble
get_col_data(seq_se)

# generate new rowdata and create a new se with the rowdata set
new_rd <- get_row_data(seq_se) %>% 
  tidyr::unite(gene_group_name, c(gene_group, gene_name))
se_new_rowdata <- set_row_data(seq_se, new_rd)

A frequently used piece of data from an se is the options contained in its coldata. cleanse offers an accessor function for this purpose:

options_from_coldata(seq_se, "site")

sessionInfo()

martijnvanattekum/cleanse documentation built on Nov. 20, 2023, 8:28 p.m.