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get_baselineCT

Source: R/get_baseline.R
get_baselineCT.Rd

get cluster-specific quantile distribution of transcript number and per cell per molecule transcript score in the provided cell x gene expression matrix based on the reference profiles and cell cluster assignment

Usage

get_baselineCT(refProfiles, counts, clust = NULL)

Arguments

refProfiles

A matrix of cluster profiles, genes X clusters

counts

Counts matrix, cells X genes.

clust

Vector of cluster assignments for each cell in counts, default = NULL to automatically assign the cell cluster for each cell based on maximum transcript score

Value

a list

  1. span_score, a matrix of average transcript tLLR score per molecule per cell for 22 distinct cell types in rows, percentile at (0%, 25%, 50%, 75%, 100%) in columns

  2. span_transNum, a matrix of transcript number per cell for each distinct cell types in row, percentile at (0%, 25%, 50%, 75%, 100%) in columns

  3. score_baseline, a named vector of 25% quantile of cluster-specific per cell transcript score, to be used as score baseline such that per cell transcript score higher than the baseline is required to call a cell type of high enough confidence

  4. lowerCutoff_transNum, a named vector of 25% quantile of cluster-specific per molecule per cell transcript number, to be used as transcript number cutoff such that higher than the cutoff is required to keep query cell as it is

  5. higherCutoff_transNum, a named vector of median value of cluster-specific per molecule per cell transcript number, to be used as transcript number cutoff such that lower than the cutoff is required to keep query cell as it is when there is neighbor cell of consistent cell type.

  6. clust_used, a named vector of cluster assignments for each cell used in baseline calculation, cell_ID in counts as name

Details

Calculate average per molecule transcript score for each cell in counts expression matrix based on the provided cluster profiles refProfiles and cluster assignment for each cell clust; then get the quantile distribution of transcript number and per molecule per cell transcript score under each cluster. The function would also recommend the cutoff for transcript score and transcript number to be used in re-segmentation pipeline based on the calculated quantile distribution.

Examples

data(example_refProfiles)
data(ori_RawExprs)
baselineData <- get_baselineCT(refProfiles = example_refProfiles, 
                               counts = ori_RawExprs, clust = NULL)
#> Found 960 common genes among `refProfiles` and `counts`. 
#> No common cell types/clusters found between `clust` and `refProfiles`.
#> Perform cluster assignment based on maximum transcript score given the provided `refProfiles`.