--- a
+++ b/man/sammy.Rd
@@ -0,0 +1,100 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/internal-functions-samr-adapted.R
+\name{sammy}
+\alias{sammy}
+\title{Significance analysis of microarrays}
+\usage{
+sammy(
+  data,
+  resp.type = c("Quantitative", "Two class unpaired", "Survival", "Multiclass",
+    "One class", "Two class paired", "Two class unpaired timecourse",
+    "One class timecourse", "Two class paired timecourse", "Pattern discovery"),
+  assay.type = c("array", "seq"),
+  s0 = NULL,
+  s0.perc = NULL,
+  nperms = 100,
+  center.arrays = FALSE,
+  testStatistic = c("standard", "wilcoxon"),
+  time.summary.type = c("slope", "signed.area"),
+  regression.method = c("standard", "ranks"),
+  return.x = FALSE,
+  knn.neighbors = 10,
+  random.seed = NULL,
+  nresamp = 20,
+  nresamp.perm = NULL,
+  xl.mode = c("regular", "firsttime", "next20", "lasttime"),
+  xl.time = NULL,
+  xl.prevfit = NULL
+)
+}
+\arguments{
+\item{data}{Data object with components x- p by n matrix of features, one
+observation per column (missing values allowed); y- n-vector of outcome
+measurements; censoring.status- n-vector of censoring censoring.status
+(1= died or event occurred, 0=survived, or event was censored), needed for a
+censored survival outcome}
+
+\item{resp.type}{Problem type: "Quantitative" for a continuous parameter
+(Available for both array and sequencing data); "Two class unpaired" (for
+both array and sequencing data); "Survival" for censored survival outcome
+(for both array and sequencingdata); "Multiclass": more than 2 groups (for
+both array and sequencing data); "One class" for a single group (only for
+array data); "Two class paired" for two classes with paired observations
+(for both array and sequencing data); "Two class unpaired timecourse" (only
+for array data), "One class time course" (only for array data),
+"Two class.paired timecourse" (only for array data), or "Pattern discovery"
+(only for array data)}
+
+\item{assay.type}{Assay type: "array" for microarray data, "seq" for counts
+from sequencing}
+
+\item{s0}{Exchangeability factor for denominator of test statistic; Default
+is automatic choice. Only used for array data.}
+
+\item{s0.perc}{Percentile of standard deviation values to use for s0; default
+is automatic choice; -1 means s0=0 (different from s0.perc=0, meaning
+s0=zeroeth percentile of standard deviation values= min of sd values.
+Only used for array data.}
+
+\item{nperms}{Number of permutations used to estimate false discovery rates}
+
+\item{center.arrays}{Should the data for each sample (array) be median
+centered at the outset? Default =FALSE. Only used for array data.}
+
+\item{testStatistic}{Test statistic to use in two class unpaired case.Either
+"standard" (t-statistic) or ,"wilcoxon" (Two-sample wilcoxon or Mann-Whitney
+test). Only used for array data.}
+
+\item{time.summary.type}{Summary measure for each time course: "slope", or
+"signed.area"). Only used for array data.}
+
+\item{regression.method}{Regression method for quantitative case: "standard",
+(linear least squares) or "ranks" (linear least squares on ranked data).
+Only used for array data.}
+
+\item{return.x}{Should the matrix of feature values be returned? Only useful
+for time course data, where x contains summaries of the features over time.
+Otherwise x is the same as the input data}
+
+\item{knn.neighbors}{Number of nearest neighbors to use for imputation of
+missing features values. Only used for array data.}
+
+\item{random.seed}{Optional initial seed for random number generator
+(integer)}
+
+\item{nresamp}{For assay.type="seq", number of resamples used to construct
+test statistic. Default 20. Only used for sequencing data.}
+
+\item{nresamp.perm}{For assay.type="seq", number of resamples used to
+construct test statistic for permutations. Default is equal to nresamp and it
+must be at most nresamp. Only used for sequencing data.}
+
+\item{xl.mode}{Used by Excel interface}
+
+\item{xl.time}{Used by Excel interface}
+
+\item{xl.prevfit}{Used by Excel interface}
+}
+\description{
+This function is an adaptation of `samr::samr`
+}