View source: R/get_edgeR_results.R
Returns an object of class topTags
containing results filtered by FDR < alpha for one comparison. get_edgeR_results_all_levels()
returns a list of topTags
objects returned by get_edgeR_results()
for all levels of the first variable in the formula.
1 2 3 4 5 6 | get_edgeR_results(formla, pseq = NYC_HANES, method = c("BH", "IHW"),
coef = 2, alph = 0.01, filtering = method[1] == "BH",
countMinimum = 8, percentMinimumHaveCount = NULL, nMinimumHaveCount = 3,
NA.RM = TRUE)
get_edger_results_all_levels(formla, ...)
|
formla |
formula. specifies the design matrix used by |
pseq |
object of class |
method |
character. Specifies the method of multiple testing correction to apply, either "BH" (Benjamini-Hochberg) or "IHW" (independent hypothesis weighting). |
coef |
integer. Specifies which linear model coefficient to test (default 2). |
alph |
numeric. Specifies what FDR level is considered alpha, and only keeps results with FDR less than this number. |
filtering |
logical. Whether or not to apply pre-filtering. |
countMinimum |
integer. If |
percentMinimumHaveCount |
numeric. If |
nMinimumHaveCount |
numeric. If |
NA.RM |
logical. Whether or not to remove samples with NA values in the |
... |
further arguments passed to |
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