Microbial 'omics


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pn-ps-data [artifact]

Table of Contents

CONCEPT

A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

🔙 To the main page of anvi’o programs and artifacts.

Provided by

anvi-get-pn-ps-ratio

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

This describes the output of anvi-get-pn-ps-ratio, which calculates the pN/pS ratio for each gene in a contigs-db.

See the page for anvi-get-pn-ps-ratio for an explanation of the pN/pS ratio

This describes a directory that contains the following four files:

pNpS.txt: a long-format table of the pN/pS values, along with the groupby variables:

  corresponding_gene_call sample_id pNpS_reference
0 1744 ANE_004_05M 0.043503524536208836
1 1744 ANE_004_40M 0.043628712253629943
2 1744 ANE_150_05M 0.03810623760551494
3 1744 ANE_150_40M 0.040815421982026576

pN.txt: a long-format table of the pN values, along with the groupby variables:

  corresponding_gene_call sample_id pN_reference
0 1744 ANE_004_05M 11.827627600424583
1 1744 ANE_004_40M 11.106801744995472
2 1744 ANE_150_05M 9.62355553228605
3 1744 ANE_150_40M 10.067364489809782

pS.txt: a long-format table of the pS values, along with the groupby variables:

  corresponding_gene_call sample_id pS_reference
0 1744 ANE_004_05M 271.87745651689016
1 1744 ANE_004_40M 254.57551165909962
2 1744 ANE_150_05M 252.54541348089631
3 1744 ANE_150_40M 246.6558962502711

num_SCVs.txt: a long-format table of the number of SCVs belonging to each group:

  corresponding_gene_call sample_id num_SCVs
0 1744 ANE_004_05M 180
1 1744 ANE_004_40M 166
2 1744 ANE_150_05M 162
3 1744 ANE_150_40M 160

Edit this file to update this information.