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Function to summarize the depth (Total that passed Q30)

Source: R/variant_summary.R
DepthSummary.Rd

This function allows you to summarize the depth

Usage

DepthSummary(path, CellSubset = NA, only_Total = T)

Arguments

path

The XX/final folder, the output from mitoV

CellSubset

A vector of ATAC cell names for subsetting, default is NA

only_Total

Default is T, Only return total depth summary. Don't care about depth in different quality filtering

Processed

Boolean variable(Default T), if true directly readRDS("depth.RDS") or, generate and saveout "depth.RDS"

Value

this returns depth which is a list of 4 list(Total/LS/S/VS), each contains 2 df, summarize mito coverage by Pos/Cell. LS = Less Stringent (was VerySensitive), S = Stringent (was Sensitive), VS = Very Stringent (was Specific). For backward compatibility, also includes VerySensitive=LS, Sensitive=S, Specific=VS. Automatically detects column formats: new (CellBC/Position/Total/VerySensitive/Sensitive/Specific), new LS/S/VS (CellBC/Position/Total/LS/S/VS), or old (V1/V2/V3/V4/V5/V6).

Examples

if (FALSE) {
WD <- "/path/to/redeemV/final"
DN1CD34_1.depth <- DepthSummary(WD)
}