omicslonda: Omics Longitudinal Differential Analysis for one feature

In aametwally/OmicsLonDA: Omics Longitudinal Differential Analysis

Description

Find significant time intervals of omic feature

Usage

omicslonda(se_object = NULL, n.perm = 500, fit.method = "ssgaussian",
  points = NULL, text = "FeatureName", parall = FALSE,
  pvalue.threshold = 0.05, adjust.method = "BH", time.unit = "days",
  ylabel = "Normalized Count", col = c("blue", "firebrick"),
  prefix = "Test")

Arguments

se_object	SummarizedExperiment object contains omics count/level matrix and metadata contains (subject, time, group, and any any other covariates)
n.perm	number of permutations.
fit.method	fitting method (ssguassian).
points	points at which the prediction should happen.
text	Feature's name.
parall	boolean to indicate whether to use multicore.
pvalue.threshold	p-value threshold cutoff for identifing significant time intervals.
adjust.method	multiple testing correction method.
time.unit	time unit used in the Time vector (hours, days, weeks, months, etc.)
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")).
prefix	prefix to be used to create directory for the analysis results

Value

a list of the significant time intervals for the tested feature, fitted model for each group, null distribution of the test statistic of the tested feature, and the original input data.

References

Ahmed Metwally ([e-mail])

Examples

library(SummarizedExperiment)
data(omicslonda_data_example)
omicslonda_se_object_adjusted = adjustBaseline(
                 se_object = omicslonda_data_example$omicslonda_se_object)
omicslonda_test_object = omicslonda_se_object_adjusted[1,]
points = seq(1, 500, length.out = 500)
res = omicslonda(se_object = omicslonda_test_object, n.perm = 10,
                 fit.method = "ssgaussian", points = points, text = "Feature_1",
                 parall = FALSE, pvalue.threshold = 0.05, 
                 adjust.method = "BH", time.unit = "days",
                 ylabel = "Normalized Count",
                 col = c("blue", "firebrick"), prefix = tempfile())

aametwally/OmicsLonDA documentation built on Feb. 10, 2020, 11:47 a.m.