In martijnvanattekum/cleanse: Tidyverse functions for SummarizedExperiment

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

Due to their unique ability to contain row- and colData, SummarizedExperiments (se's) can not be written to a delimited file using functions such as write_csv. A set of functions is provided to mimic the write_ functions of readr. Currently, read_csv, read_tsv, and read_delim can be used. To round the example seq_se and write it to a csv file, use

library(dplyr)
library(SummarizedExperiment)
library(cleanse)

data(seq_se)
seq_se %>% round(3) %>% write_csv("out.csv", "expression")

When not providing a folder, the output is written to the current working directory. The beginning of the out.csv file will look like:

EXPRESSION gene_group gene_name                            
   patient                           1      2      3      4 ...
      site                        skin   skin   skin   skin ...
      time                           0      0      0      0 ...
 treatment                           A      A      A      A ...
                   IL     IL1R1 15.053  2.617 20.093 12.464 ...
                   IL     IL1R2  4.876 16.154 19.834  6.419 ...
                  ...       ...    ...    ...    ...    ... ...