trelli_panel_by {pmartR} | R Documentation |
Set the "panel_by" variable for a trelliData object
Description
Allows for grouping omics or stats data for downstream plotting and cognostic functions
Usage
trelli_panel_by(trelliData, panel)
Arguments
trelliData |
A trelliscope data object made by as.trelliData or as.trelliData.edata. Required. |
panel |
The name of a column in trelliData to panel the data by. Required. |
Value
A trelliData object with attributes "panel_by_omics" or "panel_by_stat" to determine which columns to divide the data by.
Author(s)
David Degnan, Lisa Bramer
Examples
library(pmartRdata)
trelliData1 <- as.trelliData.edata(e_data = pep_edata,
edata_cname = "Peptide",
omics_type = "pepData")
# Transform the data
omicsData <- edata_transform(omicsData = pep_object, data_scale = "log2")
# Group the data by condition
omicsData <- group_designation(omicsData = omicsData, main_effects = c("Phenotype"))
# Apply the IMD ANOVA filter
imdanova_Filt <- imdanova_filter(omicsData = omicsData)
omicsData <- applyFilt(filter_object = imdanova_Filt, omicsData = omicsData,
min_nonmiss_anova = 2)
# Normalize my pepData
omicsData <- normalize_global(omicsData, "subset_fn" = "all", "norm_fn" = "median",
"apply_norm" = TRUE, "backtransform" = TRUE)
# Implement the IMD ANOVA method and compute all pairwise comparisons
# (i.e. leave the `comparisons` argument NULL)
statRes <- imd_anova(omicsData = omicsData, test_method = 'combined')
# Generate the trelliData object
trelliData2 <- as.trelliData(omicsData = omicsData)
trelliData3 <- as.trelliData(statRes = statRes)
trelliData4 <- as.trelliData(omicsData = omicsData, statRes = statRes)
## "panel_by" with an edata file.
trelli_panel_by(trelliData = trelliData1, panel = "Peptide")
trelli_panel_by(trelliData = trelliData1, panel = "Sample")
## "panel_by" with trelliData containing omicsData.
## Generate trelliData2 using the example code for as.trelliData
trelli_panel_by(trelliData = trelliData2, panel = "Peptide")
trelli_panel_by(trelliData = trelliData2, panel = "RazorProtein")
## "panel_by" with trelliData containing statRes.
## Generate trelliData3 using the example code for as.trelliData
trelli_panel_by(trelliData = trelliData3, panel = "Peptide")
## "panel_by" with trelliData containing both omicsData and statRes.
## Generate trelliData4 using the example code for as.trelliData
trelli_panel_by(trelliData = trelliData4, panel = "Peptide")
trelli_panel_by(trelliData = trelliData4, panel = "RazorProtein")
trelli_panel_by(trelliData = trelliData4, panel = "SampleID")
[Package pmartR version 2.4.5 Index]