In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Objective

Create a flag_tech_failure() function to allow a user to define a sample manually as a technical failure/outlier from a HermesData object.

Idea

#Creating the HermesData object from the example SummarizedExperiment object.
result <- HermesData(summarized_experiment)

#Collect sample names/IDs from the HermesData object.
samples <- colnames(object)

#Match user specified technical failure IDs to the sample IDs.
match(sample_ids, samples)

#Change technical failure flag in the HermesData object.
colData(result)$TechnicalFailureFlag[sample_ids] <- TRUE

#Putting the final function together.
flag_tech_failure <- function(object,
                              sample_ids){
  assert_that(
    is_hermes_data(object),
    is_character_vector(sample_ids)
  )
  samples <- colnames(object)
  matches <- match(sample_ids, samples)
  colData(object)$TechnicalFailureFlag[matches] <- TRUE

  object
}

insightsengineering/hermes documentation built on May 2, 2024, 6:01 a.m.