metalondaAll: Metagenomic Longitudinal Differential Abundance Analysis for...

In aametwally/MetaLonDA: Metagenomics Longitudinal Differential Abundance Method

Description

Identify significant features and their significant time interval

Usage

metalondaAll(
  Count,
  Time,
  Group,
  ID,
  n.perm = 500,
  fit.method = "nbinomial",
  num.intervals = 100,
  parall = FALSE,
  pvalue.threshold = 0.05,
  adjust.method = "BH",
  time.unit = "days",
  norm.method = "none",
  prefix = "Output",
  ylabel = "Normalized Count",
  col = c("blue", "firebrick")
)

Arguments

Count	Count matrix of all features
Time	Time label of all samples
Group	Group label of all samples
ID	individual ID label for samples
n.perm	number of permutations
fit.method	The fitting method (nbinomial, lowess)
num.intervals	The number of time intervals at which metalonda test differential abundance
parall	logic to indicate whether to use multicore
pvalue.threshold	p-value threshold cutoff
adjust.method	Multiple testing correction methods
time.unit	time unit used in the Time vector (hours, days, weeks, months, etc.)
norm.method	normalization method to be used to normalize count matrix (css, tmm, ra, log10, median_ratio)
prefix	prefix for the output figure
ylabel	text to be shown on the y-axis of all generated figures (default: "Normalized Count")
col	two color to be used for the two groups (eg., c("red", "blue")).

Value

Returns a list of the significant features a long with their significant time intervals

References

Ahmed Metwally ([e-mail])

Examples

## Not run: 
data(metalonda_test_data)
n.sample = 5
n.timepoints = 10
n.group = 2
Group = factor(c(rep(0, n.sample*n.timepoints), rep(1,n.sample*n.timepoints)))
Time = rep(rep(1:n.timepoints, times = n.sample), 2)
ID = factor(rep(1:(2*n.sample), each = n.timepoints))
points = seq(1, 10, length.out = 10)
output.nbinomial = metalondaAll(Count = metalonda_test_data, Time = Time, Group = Group,
ID = ID, n.perm = 10, fit.method =  "nbinomial", num.intervals = 100, 
parall = FALSE, pvalue.threshold = 0.05, adjust.method = "BH", 
time.unit = "hours", norm.method = "none", prefix = "Test",  time.unit = "hours", 
ylabel = "Normalized Count", col = c("black", "green"))

## End(Not run)

aametwally/MetaLonDA documentation built on Dec. 26, 2019, 7:46 a.m.