sammy {DIscBIO}

Significance analysis of microarrays

Description

This function is an adaptation of 'samr::samr'

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

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

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)

assay.type

Assay type: "array" for microarray data, "seq" for counts from sequencing

s0

Exchangeability factor for denominator of test statistic; Default is automatic choice. Only used for array data.

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.

nperms

Number of permutations used to estimate false discovery rates

center.arrays

Should the data for each sample (array) be median centered at the outset? Default =FALSE. Only used for array data.

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.

time.summary.type

Summary measure for each time course: "slope", or "signed.area"). Only used for array data.

regression.method

Regression method for quantitative case: "standard", (linear least squares) or "ranks" (linear least squares on ranked data). Only used for array data.

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

knn.neighbors

Number of nearest neighbors to use for imputation of missing features values. Only used for array data.

random.seed

Optional initial seed for random number generator (integer)

nresamp

For assay.type="seq", number of resamples used to construct test statistic. Default 20. Only used for sequencing data.

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.

xl.mode

Used by Excel interface

xl.time

Used by Excel interface

xl.prevfit

Used by Excel interface