compute_taxa_milk_association: Compute association between reads mapping to taxanomic groups...

In rbarner/infantMilkConsumption: Create statistical tables and plots used in manuscript "Formula with Added Sugars Significantly Alters Gut Microbiota and Cognitive Development in Hispanic Infants"

Description

This function will output the results of multiple statistical models determining association between taxonomic groups of gut microbiota and milk consumption type at 6-months of age.

Usage

compute_taxa_milkType_association(asfbf_fdrFile=fdrCI_lefse_phylum_level_6m_asfbf,tfbf_fdrFile = fdrCI_lefse_phylum_level_6m_tfbf, taxaFile = phylumTaxa)

Arguments

asfbf_fdrFile	R Data file containing the permuttated false discover rates for taxa differences between added-sugar formula group and breastfed groups.
tfbf_fdrFile	R Data file containing the permuttated false discover rates for taxa differences between traditional formula group and breastfed groups.
taxaFile	R Data file containing read counts of taxa at specified level with samples as columns and taxonomic groups as rows.

Value

The output will be a data frame with the following columns:

allOutcomes	Taxonomic group
bfList	Mean (Standard Deviation) of taxonomic group in breastfed group
tfList	Mean (Standard Deviation) of taxonomic group in traditional formula fed group
asfList	Mean (Standard Deviation) of taxonomic group in added-sugar formula fed group
difftfbfList	Mean difference (Lower confidence level, upper confidence level) between diversity metric in traditional formula and breastfed groups
pValTFBF_list	P-value of difference between traditional formula group and breastfed group
diffasfbfList	Mean difference (Lower confidence level, upper confidence level) between added-sugar formula group and breastfed group
pValTFBF_list	P-value of difference between added-sugar formula group and breastfed group

Author(s)

Roshonda B. Jones

Examples

compute_taxa_milkType_association()
compute_taxa_milkType_association(asfbf_fdrFile=fdrCI_lefse_genus_level_6m_asfbf,tfbf_fdrFile = fdrCI_lefse_genus_level_6m_tfbf, taxaFile = genusTaxa)

rbarner/infantMilkConsumption documentation built on Nov. 19, 2019, 12:36 a.m.