merge_samples: Merge samples that are from the sample subject

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Merge samples that are from the sample subject

Description

Merge samples that are from the sample subject

Usage

merge_samples(data_dir, merge_list, new_founder = NULL)

Arguments

data_dir	of single-cell
merge_list	Names are new name, values are current names to merge
new_founder	Name of new founder for dataset for grouping in select menu. Default (NULL) keeps previous founder.

Value

called for side effects

Examples

if (interactive()) {

  # FILL THIS IN
  sc_dir <- ''

  dataset_names <- c('SJIALD_VS_HEALTHY_merged_QC1.0_fastMNN')

  merge_list <- list(
    'SJIALD_20200716' = c('SJIALD_1-20200716_QC3.0_NO_NEUTRO', 'SJIALD_2-20200716_QC3.0_NO_NEUTRO'),
    'SJIALD_FID12518' = c('SJIALD_FID12518_Diseased_QC2.0'))

  new_founder <- 'SJIALD_VS_HEALTHY_merged'

  for (dataset_name in dataset_names) {
    data_dir <- file.path(sc_dir, dataset_name)
    merge_samples(data_dir, merge_list, new_founder)
  }

}

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.