Skip to contents

Import data from Parse (experimental)

Source: R/import_functs.R
import_data_from_parse.Rd

import_data_from_parse() imports data from the output of the Parse count matrix generation program. See Chapter 1 of the manual for more information about this function.

Usage

import_data_from_parse(
  gene_mat_fp,
  grna_mat_fp,
  all_genes_fp,
  all_grnas_fp,
  moi,
  grna_target_data_frame,
  extra_covariates = data.frame()
)

Arguments

gene_mat_fp

file path to the gene count_matrix.mtx file.

grna_mat_fp

file path to the gRNA count_matrix.mtx file.

all_genes_fp

file path to the all_genes.csv file containing the gene IDs.

all_grnas_fp

file path to the all_guides.csv file containing the gRNA IDs. The gRNA IDs are assumed to be in the second column (i.e., the "gene_name" column) of this file.

moi

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

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.

extra_covariates

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

Value

an initialized sceptre_object

Details

import_data_from_parse() is experimental, and the API of this function is subject to change. We expect the API to solidify as we learn more about the Parse platform and the structure of the Parse count matrix generation program output.

The example data shipped with the package (used in the examples below) are a small subset of Parse Biosciences' "Technical Performance of CRISPR Detect in Cell Lines" demo dataset, used under the Creative Commons Attribution 4.0 International (CC BY 4.0) license, with attribution to Parse Biosciences. See https://www.parsebiosciences.com/datasets/technical-performance-of-crispr-detect-in-cell-lines/.

Examples

directory <- paste0(
  system.file("extdata", package = "sceptre"),
  "/parse_example/"
)
gene_mat_fp <- paste0(directory, "gene_mat.mtx")
grna_mat_fp <- paste0(directory, "grna_mat.mtx")
all_genes_fp <- paste0(directory, "all_genes.csv")
all_grnas_fp <- paste0(directory, "all_grnas.csv")
grna_target_data_frame <- data.frame(
  grna_id = c("guide_A", "guide_B", "guide_C"),
  grna_target = c("target-A", "target-B", "non-targeting")
)
sceptre_object <- import_data_from_parse(
  gene_mat_fp = gene_mat_fp,
  grna_mat_fp = grna_mat_fp,
  all_genes_fp = all_genes_fp,
  all_grnas_fp = all_grnas_fp,
  moi = "low",
  grna_target_data_frame = grna_target_data_frame
)