PALMO (version 0.1.2)

longitudinalmfuzz: 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
)

Value

longitudinal trajectory dataframe

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

Examples

if (FALSE) {
longitudinalmfuzz(data_object=palmo_obj, group_column='group',
timeColumn='Time', donorColumn='PTID')
}