has_signif_negative_cluster

Classify a well as having a significant negative cluster (eg. a mutant well)
or not using a binomial test. 
We can call a well as mutant if it is statistically significantly more than
1
mutant drops, then the mutant frequency is 1.4
significantly more than 1
P(x &gt;= 7)
 = 1 - P(x &lt;= 7) + P(x = 7)
 = 1 - pbinom(7, 500, .01) + dbinom(7, 500, .01)
 = 0.237
 &gt; 0.01
So not statistically significantly enough, so we say it's a wildtype well.
But if there are 5000 drops and 70 mutant drops (same 1.4
with higher absolute numbers), then
P(x &gt;= 70) = 1 - pbinom(70, 5000, .01) + dbinom(70, 5000, .01) = 0.004
So this is indeed significant, and this well would be deemed mutant.

internal

An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for analyzing
two-channel ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
using R.

Dean Attali

ddpcr

Analysis and Visualization of Droplet Digital PCR in R and on
the Web

has_signif_negative_cluster function

<dl><dt>plate</dt>
<dd>A ddPCR plate</dd>
<dt>neg</dt>
<dd>Number of negative (or mutant) drops</dd>
<dt>pos</dt>
<dd>Number of positive (or wildtype) drops</dd></dl>

Arguments

Classify a well as having a significant negative cluster (eg. a mutant well)
or not using a binomial test. 
We can call a well as mutant if it is statistically significantly more than
1
mutant drops, then the mutant frequency is 1.4
significantly more than 1
P(x &gt;= 7)
 = 1 - P(x &lt;= 7) + P(x = 7)
 = 1 - pbinom(7, 500, .01) + dbinom(7, 500, .01)
 = 0.237
 &gt; 0.01
So not statistically significantly enough, so we say it's a wildtype well.
But if there are 5000 drops and 70 mutant drops (same 1.4
with higher absolute numbers), then
P(x &gt;= 70) = 1 - pbinom(70, 5000, .01) + dbinom(70, 5000, .01) = 0.004
So this is indeed significant, and this well would be deemed mutant.

Does a well have a statistically significant number of negative droplets? — has_signif_negative_cluster

<dl>

<dt>plate</dt>
<dd>A ddPCR plate</dd>


<dt>neg</dt>
<dd>Number of negative (or mutant) drops</dd>


<dt>pos</dt>
<dd>Number of positive (or wildtype) drops</dd>

</dl>

has_signif_negative_cluster: Does a well have a statistically significant number of negative droplets?

Description

Usage

Value

Arguments