In martijnvanattekum/cleanse: Tidyverse functions for SummarizedExperiment

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

Occasionally, we want to perform arithmetic operations on the values contained in 2 se's, for instance when subtracting control values from treated values.

If we want to subtract the values from time == 0 from the values at time == 4, this can be achieved with a combination of filter and -.
Arithmetic operations require the se's to have the same ColData and rowData. To ensure the colData is the same, we have to:

• remove the time information from colData using the select function
• rearrange the data by patient, then site, then treatment (although not strictly necessary for the example se)

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

data(seq_se)
seq_se_t0 <- seq_se %>% filter(col, time == 0) %>% 
  select(col, -time) %>% 
  arrange(col, patient, site, treatment)
assay(seq_se_t0)[1:5, 1:5]
seq_se_t4 <- seq_se %>% filter(col, time == 4) %>% 
  select(col, -time) %>% 
  arrange(col, patient, site, treatment)
assay(seq_se_t4)[1:5, 1:5]
seq_se_diff <- seq_se_t4 - seq_se_t0
assay(seq_se_diff)[1:5, 1:5]

Similarly, functions for +, /, and *, can be used.

In addition, a method to round the values from all assays is provided:

seq_se_rounded <- seq_se %>% round(3)
assay(seq_se)[1:5, 1:5]
assay(seq_se_rounded)[1:5, 1:5]

sessionInfo()

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