Clarity around logFC for gene_stats

[AMChalkie]

Hi,

1. For sgRNA the code is
   log2(est$cpm_b + 1) - log2(est$cpm_a + 1)
2. And for gene level:
   mean(logFC) of all sgRNA in that gene.

This has the unfortunate effect that if you try and re-calculate the logFC from the cpm values in the sheet level data, you get a difference. It is worth being explicit about this, or having multiple CPMs (although that would create confusion).

Best wishes
Alistair

[hyunhwaj]

Thanks for the report, and there have been some changes to clarify the logFC.

First, the logFC_level argument has been added. The default value of the argument is set to "sgRNA" (i.e. it will be set to "sgRNA" if there is no value is assigned) because to make the default mode produces the same result what the previous version had produced. In the later version, it is possible to change the default value.

CB2/man/measure_gene_stats.Rd

Line 12 in 5aeef4b

\item{logFC_level}{The level of `logFC' value. It can be `gene' or `sgRNA'.}

Second, in the documentation, I have added the detailed description as follows:

CB2/man/measure_gene_stats.Rd

Line 21 in 5aeef4b

\item `logFC': The log fold change of the gene between two groups. Taking the mean of sgRNA `logFC's is default, and `logFC` is calculated by `log2(cpm_b+1) - log2(cpm_a+1)' if `logFC_level' parameter is set to `gene'.

To test the latest version, please use devtools to install. I will submit it to cran.

Thanks,

Hyun-Hwan Jeong

[AMChalkie]

Thanks, much appreciated.

…

On Tue, 26 May 2020 at 20:00, Hyun-Hwan Jeong ***@***.***> wrote: Thanks for the report, and there have been some changes to clarify the logFC. First, the logFC_level argument has been added. The default value of the argument is set to "sgRNA" (i.e. it will be set to "sgRNA" if there is no value is assigned) because to make the default mode produces the same result what the previous version had produced. In the later version, it is possible to change the default value. https://github.com/LiuzLab/CB2/blob/5aeef4b5efd4c7ce82f9b1c11d5159d075275c97/man/measure_gene_stats.Rd#L12 Second, in the documentation, I have added the detailed description as follows: https://github.com/LiuzLab/CB2/blob/5aeef4b5efd4c7ce82f9b1c11d5159d075275c97/man/measure_gene_stats.Rd#L21 To test the latest version, please use devtools to install. I will submit it to cran. Thanks, Hyun-Hwan Jeong — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#9 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA3O2K22A2YJDJM4NEF4U3TRTOHM3ANCNFSM4NHOJFTA> .

[hyunhwaj]

It is now available in cran.