omicslonda: Omics Longitudinal Differential Analysis for one feature

Description Usage Arguments Value References Examples

View source: R/omicslonda.R

Description

Find significant time intervals of omic feature

Usage

1
2
3
4
5
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 (ametwall@stanford.edu)

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
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.