# Processing of Achilles gene effect dependency matrix for computation of common essential genes with CoRe R package

**URL:** <https://forum.depmap.org/t/processing-of-achilles-gene-effect-dependency-matrix-for-computation-of-common-essential-genes-with-core-r-package/1130>\
**Category:** Q&A\
**Tags:** portal, genetic-screens, omics\
**Created:** [January 13, 2022, 7:19pm UTC](https://forum.depmap.org/t/processing-of-achilles-gene-effect-dependency-matrix-for-computation-of-common-essential-genes-with-core-r-package/1130 "2022-01-13T19:19:33Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Mbgventer](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/mbgventer/32/182_2.png) [@Mbgventer](https://forum.depmap.org/u/Mbgventer)\
**Post date:** [January 13, 2022, 7:19pm UTC](https://forum.depmap.org/t/processing-of-achilles-gene-effect-dependency-matrix-for-computation-of-common-essential-genes-with-core-r-package/1130/1 "2022-01-13T19:19:33Z")

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Dear DepMap community,

I hope my message finds you well and healthy !! Based on a previous post regarding the exploitation of DepMap portal data, aiming to identify dependencies in specific cancer cell lines groups ([Identify conditionally essential genes in clinical subgroups of a specific cancer type](https://forum.depmap.org/t/identify-conditionally-essential-genes-in-clinical-subgroups-of-a-specific-cancer-type/1115))

I was searching about various statistical methodologies to compute common essential genes for my cell lines/groups of interest, in order then as a second step to find the context-specific remaining essential genes, and to further validate initial approaches through using the portal;

On this premise, I found the relative R package CoRe ([CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens | BMC Genomics | Full Text](https://dx.doi.org/10.1186%2Fs12864-021-08129-5)) which includes a specific function called _ **FiPer** _, for computation of common essential genes; As I got the following feedback from the authors:

_**"The FiPer method works directly on a quantitative matrix of log fold changes/dependencies. The only preprocessing step I would recommend is to scale the essentiality profiles cell-wise using the CoRe.scale\_to\_essentials function. For this function to work, you need a character vector of a priori known essential (BAGEL\_essential and BAGEL\_nonEssential available as data object in the package) and nonessential genes and unscaled matrix. This is a normalization procedure to obtain the median of those essential genes at -1 and the median of those non-essential at 0"**_

Thus, my main question is the following: does the latest **Achilles\_gene\_effect.csv** matrix been scaled or processed in a similar way? From a small attached histogram, it seems that is has been similarly transformed, but I wanted to be certain that I could utilize the input as it is?

![Histogram.Achilles.GeneEffect](https://canada1.discourse-cdn.com/flex035/uploads/depmap/original/1X/b1b061893093005c488fd15278fd36d7f9299fa3.jpeg)

Thank you in advance for your time and consideration 🙂

Kind Regards,

Efstathios

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**Author:** ![Joshua\_Dempster](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/joshua_dempster/32/19_2.png) [@Joshua\_Dempster](https://forum.depmap.org/u/Joshua_Dempster)\
**Post date:** [January 19, 2022, 10:18pm UTC](https://forum.depmap.org/t/processing-of-achilles-gene-effect-dependency-matrix-for-computation-of-common-essential-genes-with-core-r-package/1130/2 "2022-01-19T22:18:55Z")

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Hi Efstathios,

Chronos data has not been scaled in quite the same way, but the subtle difference shouldn’t impede that function. In fact, I believe the FiPeR method is an R implementation of the method we are already using to generate the file Achilles\_common\_essentials, so it should give a very similar list of genes (modulo the default parameters and some implementation details).

Best,

Josh

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**Author:** ![Mbgventer](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/mbgventer/32/182_2.png) [@Mbgventer](https://forum.depmap.org/u/Mbgventer)\
**Post date:** [January 19, 2022, 11:00pm UTC](https://forum.depmap.org/t/processing-of-achilles-gene-effect-dependency-matrix-for-computation-of-common-essential-genes-with-core-r-package/1130/3 "2022-01-19T23:00:31Z")

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Dear Joshua,

thank you very much for your response and feedback !!