read_ondisc_backed_sceptre_object: Write or read an 'ondisc'-backed 'sceptre_object'

In Katsevich-Lab/sceptre: Analysis of Single-Cell CRISPR Screen Data

Write or read an ondisc-backed sceptre_object

Description

write_ondisc_backed_sceptre_object() and read_ondisc_backed_sceptre_object() enable the writing and reading of ondisc-backed sceptre_objects, respectively. First, write_ondisc_backed_sceptre_object() writes an ondisc-backed sceptre_object to disk, creating a file sceptre_object.rds in the specified directory. Next, read_ondisc_backed_sceptre_object() reads and initializes a sceptre_object from a sceptre_object.rds file, response.odm file, and grna.odm file stored on disk.

Usage

read_ondisc_backed_sceptre_object(
  sceptre_object_fp,
  response_odm_file_fp,
  grna_odm_file_fp
)

write_ondisc_backed_sceptre_object(sceptre_object, directory_to_write)

Arguments

sceptre_object_fp	file path to a sceptre_object.rds file
response_odm_file_fp	file path to the backing .odm file for the response modality
grna_odm_file_fp	file path to the backing .odm file for the gRNA modality
sceptre_object	a sceptre_object
directory_to_write	the directory in which to write the sceptre_object.rds file

Value

write_ondisc_backed_sceptre_object() returns NULL, and read_ondisc_backed_sceptre_object() returns an ondisc-backed sceptre_object

Examples

library(sceptredata)
data(lowmoi_example_data)
# 1. create ondisc-backed sceptre_object
sceptre_object <- import_data(
  response_matrix = lowmoi_example_data$response_matrix,
  grna_matrix = lowmoi_example_data$grna_matrix,
  grna_target_data_frame = lowmoi_example_data$grna_target_data_frame,
  extra_covariates = lowmoi_example_data$extra_covariates,
  moi = "low",
  use_ondisc = TRUE,
  directory_to_write = tempdir()
)

# 2. write
write_ondisc_backed_sceptre_object(
  sceptre_object = sceptre_object,
  directory_to_write = tempdir()
)

# 3. read
rm(sceptre_object)
sceptre_object <- read_ondisc_backed_sceptre_object(
  sceptre_object_fp = paste0(tempdir(), "/sceptre_object.rds"),
  response_odm_file_fp = paste0(tempdir(), "/response.odm"),
  grna_odm_file_fp = paste0(tempdir(), "/grna.odm")
)

Katsevich-Lab/sceptre documentation built on Nov. 24, 2024, 9:28 a.m.