Improve summaryRuns description

[mgb1985]

Hi!
With the summaryRuns function, I guessed that what is obtained with $summary_ROH_mean_chr is the mean length of runs per chromosome and group (because it is the fifth element of the summary list and in the help page of summaryRuns it's written that it is what the fifth element is).
But in the tutorial, it is written, talking about the various sumstats obtained with summaryRuns:
"Or, the average number of ROH per chromosome and per breed can be obtained.
summaryList$summary_ROH_mean_chr".
Which is clearly not the same!
So I was wondering, what is summary_ROH_mean_chr? Is it mean count or mean length? If length, what is the unit?
Thanks!
Muriel

[bunop]

Hi @mgb1985 ,

Thank you for your interest in detectRUNs. Regarding your question:

I guessed that what is obtained with $summary_ROH_mean_chr is the mean length of runs per chromosome and group (because it is the fifth element of the summary list and in the help page of summaryRuns it's written that it is what the fifth element is).

Your supposition is correct, here you can find how this value is calculated. This value is the mean length expressed in MB. You can proof it by selecting, for examples, all the runs for Jacobs and chrom 2: if you calculate the average of lengthBps column and divide by 1e6

 > mean(slidingRuns[(slidingRuns$group=="Jacobs" & slidingRuns$chrom==2),"lengthBps"]) / 1e6
[1] 4.069597

You will obtain the same value calculated for the chrom 2 and Jacobs that you see in the vignette for summaryList$summary_ROH_mean_chr label:

##   chrom   Jacobs Navajo-Churro
## 1     2 4.069597      4.492243
## 2    24 3.697987      2.745963

I Think that the example explained in the vignetted is not describe correctly. @filippob , what do you think? should summaryRuns be described better in both vignette and docs?

[mgb1985]

Hi @bunop !

Thanks for the link on the calculation!
It's all clear now!

Muriel