create_fce: Create a functional cell experiment (fce) object as a...

Description Usage Arguments Value

View source: R/utils.R

Description

Create a functional cell experiment (fce) object as a MultiAssayExperiment

Usage

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create_fce(rna_data, functional_data, id_from_name = TRUE,
  id_delim = ".", id_fields = 2, adduct_positions = NULL)

Arguments

rna_data

UMI count matrix

functional_data

Functional count matrix

id_from_name

Extract sample id from cell name (default = TRUE) If false then the sample_id field will be populated with NA.

id_delim

delimiter to split cell name (default = ".")

id_fields

index(es) of fields to extract from name for determining sample id from name (defaults to c(2))

adduct_positions

optional data.frame with positions of first and second adducts in each hairpin, must be a three column data.frame with the first column named hairpin containing with entries that match the adducts from haircut_data (i.e. Uracil from entry Uracil_1), a second column named adduct_position1 with the first adduct position, and a third column named adduct_position2 with the second adduct position

Value

fce object of class MultiAssayExperiment containing SingleCellExperiments. mRNA data is stored in slot "sce", and functional data is stored in slot "fsce"


hesselberthlab/scrunchy documentation built on Dec. 11, 2018, 1:30 a.m.