scsaStats: SCSA statistics calculator

In chadsmith123/scsa: Analysis of Sperm Chromatin Structure Assay (SCSA) Flow Cytometry Data

Description

Calcuates SCSA statistics for a sample.

Usage

scsaStats(x, id = x$id, thresh.alphat, thresh.HDS, ...)

Arguments

x	list from scsaDat output
id	sample id
thresh.alphat	Alphat threshold value. If not specified, a plot will be generated for the user to select the threshold.
thresh.HDS	High DNA Staining threshold value. If not specified, a plot will be generated for the user to select the threshold.
...	additional arguments to be passed

Details

DNA Fragmentation index (DFI) = proportion of cells above the Alphat threshold

High DNA Stainability (HDS) = proportion of cells above the HDS threshold

N = total number of cells analyzed

X.alphat = Weighted mean DFI of all cells analyzed

sd.alphat = Standard deviation of the DFI of all cells analyzed

n.comp = number of cells above the Alphat threshold

X.comp = weighted mean DFI of cells above the Alphat threshold

sd.comp = standard deviation of DFI above the Alphat threshold

thresh.alphat = user-selected Alphat threshold

thresh.HDS = user-selected HDS threshold

X.red = mean red fluorescence of all cells

X.green = mean green fluorescence of all cells

Value

Returns a list of SCSA statistics

References

Evenson DP, Larson KL, Jost LK (2002) Sperm Chromatin Structure Assay: Its Clinical Use for Detecting Sperm DNA Fragmentation in Male Infertility and Comparisons With Other Techniques. Journal of Andrology, 23, 25–43.

See Also

scsa, scsaDat, findHDS, findAlphat

Examples

data(zf_facs)
x <- scsaDat(zf_facs)
scsaStats(x,id="Sample 1",thresh.alphat=0.27,thresh.HDS=527)
# Values for SCSA thresholds can be manually entered to generate the statistics.

chadsmith123/scsa documentation built on May 13, 2019, 3:09 p.m.