setup_data {gimap} | R Documentation |
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
)
[Package gimap version 1.1.1 Index]