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Import data

Source: R/import_functs.R
import_data.Rd

import_data() imports data from a collection of R objects to create a sceptre_object. Users can create either a standard sceptre object or an ondisc-backed sceptre object; the latter is more appropriate for large-scale data. See Chapter 1 of the manual for more detailed information about this function.

Usage

import_data(
  response_matrix,
  grna_matrix,
  grna_target_data_frame,
  moi,
  extra_covariates = data.frame(),
  response_names = NA_character_,
  use_ondisc = FALSE,
  directory_to_write = NULL
)

Arguments

response_matrix

a matrix of response UMI counts, with responses in rows and cells in columns. The matrix should be of type "matrix", "dgCMatrix", "dgRMatrix", or "dgTMatrix". The row names of the matrix should give the response IDs.

grna_matrix

a matrix of gRNA UMI counts, with gRNAs in rows and cells in columns. The matrix should be of type "matrix", "dgCMatrix", "dgRMatrix", or "dgTMatrix". The row names of the matrix should give the gRNA IDs.

grna_target_data_frame

a data frame containing columns grna_id and grna_target mapping each individual gRNA to its target. Non-targeting gRNAs should be assigned a label of "non-targeting". Optionally, grna_target_data_frame can contain columns chr, start, and end, giving the chromosome, start coordinate, and end coordiante, respectively, of each gRNA. Additionally, grna_target_data_frame can contain the column vector_id specifying the vector to which a given gRNA belongs.

moi

a string indicating the MOI of the dataset, either "low" or "high".

extra_covariates

(optional) a data frame containing extra covariates (e.g., batch, biological replicate) beyond those that sceptre can compute.

response_names

(optional) a vector of human-readable response names; names with the prefix "MT-" are taken as mitochondrial genes and are used to compute the covariate response_p_mito.

use_ondisc

(default FALSE) a logical value (i.e., TRUE or FALSE) indicating whether to create an ondisc-backed sceptre_object (TRUE) or a standard sceptre_object (FALSE).

directory_to_write

(optional) a file path to a directory in which to write the backing .odm files for the response and gRNA expression matrices. Must be supplied if use_ondisc is set to TRUE.

Value

an initialized sceptre_object

Examples

data("lowmoi_example_data")
# 1. initialize a standard sceptre_object from R objects
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"
)

# 2. initialize an ondisc-backed sceptre_object from R objects
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()
)