setup_data: Making a new gimap dataset

In gimap: Calculate Genetic Interactions for Paired CRISPR Targets

Making a new gimap dataset

Description

This function allows people to have their data ready to be processed by gimap

Usage

setup_data(counts = NULL, pg_ids = NULL, sample_metadata = NULL)

Arguments

counts	a matrix of data that contains the counts where rows are each paired_guide target and columns are each sample
pg_ids	the pgRNA IDs: metadata associated with the pgRNA constructs that correspond to the rows of the counts data
sample_metadata	metadata associated with the samples of the dataset that correspond to the columns of the counts data. Should include a column that has replicate information as well as a column that contains timepoint information respectively (this will be used for log fold calculations). These columns should be factors.

Value

A special gimap_dataset to be used with the other functions in this package.

Examples

counts <- get_example_data("count", data_dir = tempdir()) %>%
  dplyr::select(c(
    "Day00_RepA", "Day05_RepA", "Day22_RepA", "Day22_RepB",
    "Day22_RepC"
  )) %>%
  as.matrix()

pg_ids <- get_example_data("count", data_dir = tempdir()) %>%
  dplyr::select("id")

sample_metadata <- data.frame(
  col_names = c("Day00_RepA", "Day05_RepA", "Day22_RepA", "Day22_RepB", "Day22_RepC"),
  day = as.numeric(c("0", "5", "22", "22", "22")),
  rep = as.factor(c("RepA", "RepA", "RepA", "RepB", "RepC"))
)

gimap_dataset <- setup_data(
  counts = counts,
  pg_ids = pg_ids,
  sample_metadata = sample_metadata
)

gimap documentation built on June 8, 2025, 10:13 a.m.