microbiome_pipeline: Microbiome analysis pipeline

In microsud/microbiomeutilities-shiny: microbiomeutilities: An R package with utility functions for the microbiome R package

Description

Function microbiome_pipeline generates an HTML report with preliminary QC, Alpha Diversity, Ordination and Composition analysis of OTU tables. This function save all intermediate files incuding figures and phyloseq objects in user specified directory.

Usage

microbiome_pipeline(otufile, mapping, taxonomy, treefilename, type, work_dir,
  out_dir, VariableA, VariableB, UnConstOrd, heatmap, filterCount, filterPrev,
  col.palette, filterpseq, samsize, projectname, author)

Arguments

otufile	biom object, otu_table in csv format or mothur shared files.
mapping	Metadata variable to check for groups based sequencing effort csv format.
taxonomy	NULL or csv fomatted file.
treefilename	for phylogenetic based diversity analysis "*.tre" file
type	"biom", "mothur", "simple" simple is for *.csv file.
work_dir	Working directory where input files are stored.
out_dir	Output directory where all outputs are to be stored.
VariableA	Main variable of interest.
VariableB	Secondary variable of interest.
UnConstOrd	If unconstrained ordination to be plotted TRUE or FALSE.
heatmap	Heatmap or not option is TRUE or FALSE.
filterCount	Filter OTUs below this count number.
filterPrev	Filter OTUs not detected in less than this percent of samples.
col.palette	= 'Spectral', 'Set2', 'Paired' use any of the RColorbrewer palette depending on number of groups you have in VaraibleA.
filterpseq	TRUE or FALSE.
samsize	Number of reads to rarefy your data and save the rarefied phyobject.
projectname	Name of the project.
author	Name of the author/investigator.

Value

A HTML report with graphs and data stats.

Author(s)

Contact: Sudarshan Shetty [e-mail]

Examples

## Not run: 

library(microbiomeutilities)
library(microbiome)
microbiome_pipeline(otufile = "my.biom",
                   mapping = "mymap.csv",
                   taxonomy = NULL,
                   treefilename = "myTree.tre",
                   type = "biom",
                   work_dir = "F:/path/my/input/filefolder",
                   out_dir = "F:/path/to/save/my/files/folder",
                   VariableA = "MC_type1",
                   VariableB = "Region",
                   UnConstOrd = TRUE,
                   heatmap = TRUE,
                   filterCount = 4,
                   filterPrev = 0.01,
                   col.palette = "Paired",
                   filterpseq = TRUE,
                   samsize = NA,
                   projectname = "Mock",
                   author = "Sudarshan")
                   
## End(Not run)

microsud/microbiomeutilities-shiny documentation built on May 7, 2019, 9:38 a.m.