tabulateFlowHist: exportFlowHist

In flowPloidy: Analyze flow cytometer data to determine sample ploidy

Description

Extract analysis results from a FlowHist object

Usage

tabulateFlowHist(fh, file = NULL)

Arguments

fh	a FlowHist object, or a list of FlowHist objects.
file	character, the name of the file to save data to

Details

A convenience function for extracting the results of the NLS curve-fitting analysis on a FlowHist object.

If fh is a single FlowHist object, a data.frame with a single row is returned. If fh is a list of FlowHist objects, a row for each object will be added to the data.frame.

If a file name is provided, the data will be saved to that file.

The columns of the returned data.frame may include:

StdPeak:

which peak (A, B etc) was identified by the user as the internal standard

ratio:

the ratio of the sample peak size to the standard peak size, if the standard size was set and the standard peak identified

StdSize:

the size of the standard in pg, if set

pg:

genome size estimate, if the sample peak was identified and the size of the standard was set

RCS:

the residual Chi-Square for the model fit

a_mean, b_mean etc:

the peak position for the G1 peak of each sample

a_stddev, b_stddev etc:

standard devation for each G1 peak position

a1_count, b1_count etc:

the cell counts for the G1 peak of each sample

a2_count, b2_count etc:

the cell counts for the G2 peak of each sample

a_s_count, b_s_count etc:

the cell counts for the S-phase for each sample

a_CV, b_CV etc:

the coefficient of variation for each sample

linearity:

the linearity value, if not fixed at 2

Note that columns are only produced for parameters that exist in your data. That is, if none of your samples have a G2 peak for the A sample, you won't get a2_count column. Similarly, if you didn't set the standard size, or identify which peak was the standard, you won't get StdPeak, ratio, StdSize, or pg columns.

Value

a data frame

Author(s)

Tyler Smith

Examples

library(flowPloidyData) 
fh1 <- FlowHist(file = flowPloidyFiles()[1], channel = "FL3.INT.LIN")
fh1 <- fhAnalyze(fh1)
tabulateFlowHist(fh1)

flowPloidy documentation built on Nov. 8, 2020, 8:04 p.m.