Description Usage Arguments Value References Examples
Identify significant features and their significant time interval
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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")
)
|
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")). |
Returns a list of the significant features a long with their significant time intervals
Ahmed Metwally (ametwall@stanford.edu)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
|
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