baxter_data: Microbiome data

In partition: Agglomerative Partitioning Framework for Dimension Reduction

Microbiome data

Description

Clinical and microbiome data derived from "Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions" by Baxter et al. (2016). These data represent a subset of 172 health participants. baxter_clinical contains 8 clinical variables for each of the participants: sample_name, id, age, bmi, gender, height, total_reads, and disease_state (all H for healthy). baxter_otu has 1,234 columns, where each columns represent an Operational Taxonomic Unit (OTU). OTUs are species-like relationships among bacteria determined by analyzing their RNA. The cells are logged counts for how often the OTU was detected in a participant's stool sample. Each column name is a shorthand name, e.g. otu1; you can find the true name of the OTU mapped in baxter_data_dictionary. baxter_family and baxter_genus are also logged counts but instead group OTUs at the family and genus level, respectively, a common approach to reducing microbiome data. Likewise, the column names are shorthands, which you can find mapped in baxter_data_dictionary.

Usage

baxter_clinical

baxter_otu

baxter_family

baxter_genus

baxter_data_dictionary

Format

5 data frames

An object of class tbl_df (inherits from tbl, data.frame) with 172 rows and 1234 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 172 rows and 35 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 172 rows and 82 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 1351 rows and 3 columns.

Source

Baxter et al. (2016) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s13073-016-0290-3")}

partition documentation built on Oct. 9, 2024, 5:10 p.m.