pmartR (version 2.4.6)

as.trelliData.edata: Generate an object from edata to pass to trelliscope building functions

Description

The only acceptable input file type is a single edata file. Transformation and normalization must be specified. Isobaric protein or NMR data does not need to be normalized.

Usage

as.trelliData.edata(
  e_data,
  edata_cname,
  omics_type,
  data_scale_original = "abundance",
  data_scale = "log2",
  normalization_fun = "global",
  normalization_params = list(subset_fn = "all", norm_fn = "median", apply_norm = TRUE,
    backtransform = TRUE),
  is_normalized = FALSE,
  force_normalization = FALSE
)

Value

An object of class 'trelliData' containing the raw data. To be passed to trelliscope building functions.

Arguments

e_data

a \(p * (n + 1)\) data.frame of expression data, where \(p\) is the number of biomolecules observed and \(n\) is the number of samples (an additional biomolecule identifier/name column should also be present anywhere in the data.frame). Each row corresponds to data for one biomolecule. One column specifying a unique identifier for each biomolecule (row) must be present. We do not recommend passing data that requires reference normalization (isobaric, nmr, etc.)

edata_cname

character string specifying the name of the column containing the biomolecule identifiers. It should be the only non-numeric colummn in edata.

omics_type

A string specifying the data type. Acceptable options are "pepData", "isobaricpepData", "proData", "metabData", "lipidData", "nmrData", or "seqData".

data_scale_original

A character string indicating original scale of the data. Valid values are: 'log2', 'log', 'log10', or 'abundance'. Default is abundance. This parameter is ignored if the data is "seqData".

data_scale

A character string indicating the scale to transform the data to. Valid values are: 'log2', 'log', 'log10', or 'abundance'. If the value is the same as data_scale_original, then transformation is not applied. Default is log2. This parameter is ignored if the data is "seqData".

normalization_fun

A character string indicating the pmartR normalization function to use on the data, if is_normalized is FALSE. Acceptable choices are 'global', 'loess', and 'quantile'. This parameter is ignored if the data is "seqData".

normalization_params

A vector or list where the normalization parameters are the names, and the parameter values are the list values. For example, an acceptable entry for 'normalize_global' would be list("subset_fn" = "all", "norm_fn" = "median", "apply_norm" = TRUE, "backtransform" = TRUE). This parameter is ignored if the data is "seqData".

is_normalized

A logical indicator of whether the data is already normalized (and will therefore skip the normalization step). This parameter is ignored if the data is "seqData".

force_normalization

A logical indicator to force normalization that is not required for both isobaric protein and NMR data. This parameter is ignored if the data is "seqData."

Author

David Degnan, Daniel Claborne, Lisa Bramer

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
library(pmartRdata)

###########################
## MS/NMR OMICS EXAMPLES ##
###########################

# Simple MS/NMR Example 
trelliData1 <- as.trelliData.edata(e_data = pep_edata,
                                   edata_cname = "Peptide",
                                   omics_type = "pepData")
 
######################
## RNA-SEQ EXAMPLES ##  
######################
                                    
# RNA-seq Example
trelliData_seq1 <- as.trelliData.edata(e_data = rnaseq_edata, 
                                      edata_cname = "Transcript",
                                      omics_type = "seqData")
                                  
          
}