merge_two_expfiles: Merge two exp files

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Merge two exp files

Description

merge_two_expfiles Used to combine two single cell type datasets.

Usage

merge_two_expfiles(
  exp1,
  exp2,
  annot1,
  annot2,
  name1 = "",
  name2 = "",
  as_sparse = TRUE,
  as_DelayedArray = FALSE,
  verbose = TRUE
)

Arguments

exp1	Numerical expression matrix for dataset1 with row for each gene and column for each cell. Row names are gene symbols. Column names are cell IDs which can be cross referenced against the annot data frame.
exp2	Numerical expression matrix for dataset2 with row for each gene and column for each cell. Row names are gene symbols. Column names are cell IDs which can be cross referenced against the annot data frame.
annot1	Annotation data frame for dataset1 which contains three columns at least: cell_id, level1class and level2class
annot2	Annotation data frame for dataset2 which contains three columns at least: cell_id, level1class and level2class
name1	Name used to refer to dataset 1. Leave blank if it's already a merged dataset.
name2	Name used to refer to dataset 2. Leave blank if it's already a merged dataset.
as_sparse	Convert the merged exp to a sparse matrix.
as_DelayedArray	Convert the merged exp to a DelayedArray.
verbose	Print messages.

Value

List containing merged exp and annot.

Examples

cortex_mrna <- ewceData::cortex_mrna()
exp1 <- cortex_mrna$exp[, 1:50]
exp2 <- cortex_mrna$exp[, 51:100]
annot1 <- cortex_mrna$annot[1:50, ]
annot2 <- cortex_mrna$annot[51:100, ]
merged_res <- EWCE::merge_two_expfiles(
    exp1 = exp1,
    exp2 = exp2,
    annot1 = annot1,
    annot2 = annot2,
    name1 = "dataset1",
    name2 = "dataset2"
)

NathanSkene/EWCE documentation built on Nov. 3, 2024, 8:16 a.m.