getInput: Formatting input data by combine gene counts with cell cycle...

In haiyueliu/Eskrate: Estimate time-dependent RNA kinetics

Formatting input data by combine gene counts with cell cycle time

Description

Formatting input data by combine gene counts with cell cycle time

Usage

getInput(
  rawCountsLabeledMature,
  rawCountsUnlabeledMature,
  rawCountsLabeledPrecursor,
  rawCountsUnlabeledPrecursor,
  cells,
  labelingTime
)

Arguments

rawCountsLabeledMature	a data frame count gene expression matrix of labeled mature RNAs, rownames are genes are colnames are cells.
rawCountsUnlabeledMature	a data frame count gene expression matrix of unlabeled mature RNAs, rownames are genes are colnames are cells.
rawCountsLabeledPrecursor	a data frame count gene expression matrix of unlabeled precursor RNAs, rownames are genes are colnames are cells.
rawCountsUnlabeledPrecursor	a data frame count gene expression matrix of unlabeled precursor RNAs, rownames are genes are colnames are cells.
labelingTime	numeric the 4sU labeling time for the cells
cellInfo	a data frame with columns: cell_id (unique cell id) cc_Time (cell cycle time in minutes)

Value

a data frame with columns: gene, cc_time, labeling_time, p_u, p_total, m_u, m_total, captureEfficiencyPerCell

Examples

observedData <- getInput(rawCounts = raw_counts, cellInfo=cells_info)

haiyueliu/Eskrate documentation built on Sept. 3, 2023, 3:33 p.m.