| p values |
A numeric vector of raw p-values. |
| z values |
A numeric vector of Z-values to be used in pi0 estimation |
|
or a string with options “two.sided”, “greater” or “less”. Defaults to “two.sided”. |
| threshold |
A numeric value in the interval [0,1] used in a multiple comparisons |
|
hypothesis tests to determine significance from the null. Defaults to 0.05. |
| adjust.method |
A string used to identify the adjustment method. Defaults to
BH.
|
|
Options are
BH,
BY,
Bon,
Holm,
Hoch, and
Sidak.
|
| BY.corr |
A string of either “positive” or “negative” to determine which correlation |
|
is used in the BY method. Defaults to
positive.
|
| just.fdr |
A Boolean TRUE or FALSE value which output only the FDR vector instead of |
|
the list output. Defaults to FALSE. |
| default.odds |
A numeric value determining the ratio of pi1/pi0 used in the computation of |
|
single lower bound FDR. Defaults to 1. |
| estim.method |
A string used to determine which method is used to estimate |
|
the null proportion or pi0 value. Defaults to set.pi0. |
| set.pi0 |
A numeric value to specify a known or assumed pi0 value in the interval [0,1]. |
|
Defaults to 1. Which means the assumption is that all inputted raw p-values come from |
|
the null distribution. |
| hist.breaks |
A numeric or string variable representing how many breaks are used in the pi0 |
|
estimation histogram methods. Defaults to “scott”. |
| ties.method |
A string a character string specifying how ties are treated. Options are ”first”, |
|
”last”, ”average”, ”min”, ”max”, or ”random”. Defaults to ”random”. |
| sort.results |
A Boolean TRUE or FALSE value which sorts the output in either increasing or |
|
non-increasing order dependent on the FDR vector. Defaults to FALSE. |
| na.rm |
A Boolean TRUE or FALSE value indicating whether NA’s should be removed from |
|
the inputted raw p-value vector before further computation. Defaults to TRUE. |
