annotateMetadata: annotateMetadata Function

In aifimmunology/PALMO: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

annotateMetadata Function

Description

This function allows to add user-defined sample, participant, and time column to a PALMO object in standard format.

Usage

annotateMetadata(
  data_object,
  sample_column = "Sample",
  donor_column = "PTID",
  time_column = "Time",
  group_column = NULL
)

Arguments

data_object	Input PALMO S4 object. Contains annotation table and expression matrix or data frame. Rows represent gene/proteins column represents participant samples (same as annotation table Sample column)
sample_column	Name of Sample column in user input annotation data frame. Default 'Sample'
donor_column	Name of Donor/participant column in user input annotation data frame. Default 'PTID'
time_column	Name of Time column in user input annotation data frame. Default 'Time'
group_column	Optional. Calculate average expression by given group like 'celltype' or 'cluster'

Value

PALMO object

Examples

## Not run: 
annotateMetadata(data_object=palmo_obj, sample_column='Sample',
donor_column='PTID', time_column='Time')

## End(Not run)

aifimmunology/PALMO documentation built on Oct. 21, 2022, 7:39 p.m.