longitudinalmfuzz: longitudinalmfuzz Function

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

longitudinalmfuzz Function

Description

This function allows you to identify gene/feature trajectory over longitudinal points. The function uses mfuzz package (for more information refer to https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html)

Usage

longitudinalmfuzz(
  data_object,
  group_column = "group",
  timeColumn = "Time",
  timeOrder = NULL,
  donorColumn = "PTID",
  baseline_timepoint = NULL,
  featurelist = NULL,
  group_oi = NULL,
  mfuzz_thres = 0.25,
  mfuzz_min.std = 0,
  max_cluster = NULL,
  delta = 0.5,
  plotsize = 10,
  cl = 2,
  fileName = NULL,
  filePATH = NULL
)

Arguments

data_object	Input PALMO S4 object. It contains annotation information and expression data from Bulk or single cell data.
group_column	User-defined group name like 'group','celltype'
timeColumn	User-defined time column name like 'Time'
timeOrder	(Optional) User-defined order of time variable like ('D1','D2','D3')
donorColumn	User-defined donor/participant column name like 'PTID'
baseline_timepoint	(Optional) If baseline donors known (like 'PTID1')
featurelist	(Optional) User-defined genes/features of interest
group_oi	User-defined groups to consider for example from celltypes select few
mfuzz_thres	mfuzz:thres threshold for excluding genes
mfuzz_min.std	mfuzz:min.std threshold for minimum standard deviation
max_cluster	Number of clusters to explore (Default 2^n)
delta	mfuzz:delta threshold for minimum standard deviation
plotsize	Size of plot width and height. Default 10 (in).
cl	Number of clusters. Use nCores-1 to run parallel. Default 2
fileName	User-defined file name, Default outputFile
filePATH	User-defined output directory PATH Default, current directory

Value

longitudinal trajectory dataframe

Examples

## Not run: 
longitudinalmfuzz(data_object=palmo_obj, group_column='group',
timeColumn='Time', donorColumn='PTID')

## End(Not run)

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