MIMOSA (version 1.10.2)

ConstructMIMOSAExpressionSet: A wrapper for constructing an Expression Set for MIMOSA

Description

Calls a series of other functions that will reshape and refactor the data frame into the right format for use by MIMOSA Standardized for use with internal SCHARP data sets. We provide some default arguments as examples. Currently slow, and very much prototype code.

Usage

ConstructMIMOSAExpressionSet(thisdata, reference = quote(STAGE %in% "CTRL" & PROTEIN %in% "Media+cells"), measure.columns = c("Neg", "Pos"), other.annotations = setdiff(colnames(thisdata), measure.columns), default.cast.formula = component ~ ..., .variables = quote(.(PTID, TESTDT, ASSAYID, PLATEID)), featureCols = 1, ref.append.replace = "_NEG")

Arguments

thisdata

is the input data frame

reference

is an expression that evaluates to a logical vector which specifices the observations in the data frame that are to be used for the negative control or reference set

measure.columns

is a chracter vector that specifies which columns hold the observed counts

other.annotations

is a character vector that specifies which additional columns in the data frame should be included in the returned data. By default we take everything, but you could specify only relevant phenotypic information.

default.cast.formula

is a formula that tells reshape how to recast the data frame so that rows corresponde to different measured components and columns correspond to samples. By default component~... will put the components as the rows (i.e. positive and negative cell counts) and all measured phenotypic information on the columns.

.variables

is a dotted list that specifies the variable names (columns of the data frame) by which to group the data when organzing stimulated and unstimulated observations. i.e. PTID x ANTIGEN x TCELLSUBSET x TESTDT, or something else for your own data.

featureCols

is a numeric vector that specifies the indices of the columns to be used to name the features. If the casting formula is component~... then there is only one feature column (and it is the first one), so featureCols = 1, by default.

ref.append.replace

the terminating character string in the column names of the negative controls. It will be replaces with _REF for 'reference'

Examples

data(ICS)
E<-ConstructMIMOSAExpressionSet(ICS,
  reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
  other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
  default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
  .variables=.(TCELLSUBSET,CYTOKINE,UID),
  featureCols=1,ref.append.replace='_REF')