sclongitudinalDEG: sclongitudinalDEG Function

View source: R/sclongitudinalDEG.R

sclongitudinalDEGR Documentation

sclongitudinalDEG Function

Description

This function allows ser to calculate differential expressed genes in the direction of given time points (if timepoints>3 otherwise DEGs between two timepoints). A hurdle model was fit to each participant independently in order to identify participant-specific longitudinal transcriptomic changes. Genes that were expressed in at least 10% of cells per participant were considered for this analysis. The models were fit on the input normalized data, modeling the timepoints as a continuous variable within each cell type and adjusting for the batch only if any timepoints from the same participant were run across multiple batches.

Usage

sclongitudinalDEG(
  data_object,
  scassay = "RNA",
  group_column,
  group_oi = NULL,
  mincellsexpressed = 0.1,
  removelnc = "TRUE",
  adjfac = NULL,
  baseline = NULL,
  addCDR = FALSE,
  CDR_column = NULL,
  plotWidth = 10,
  plotHeight = 10,
  fileName = NULL,
  filePATH = NULL
)

Arguments

data_object

Input PALMO S4 object. It contains annotation information and expression data from Bulk or single cell data.

scassay

Single cell assay from scRNA seurat object (Default "RNA")

group_column

Column of interest such as "celltype" to analyze DEGs in participant over time

group_oi

Features of interest such as specific celltypes c("CD4_Naive", "CD4_TEM")

mincellsexpressed

Average expression threshold to filter lowly expressed genes/features Default is 0.1

removelnc

Remove lincRNAs, mitochondrial and ribosomal genes from analysis incldes (^RP|^MT-|^LINC|orf) (TRUE/FALSE). Default is TRUE

adjfac

Factors to be adjusted for such as batch, sex

baseline

Donors (PTID) to be considered as baseline. Deafult NULL

addCDR

(Optional) Add CDR while performing differential analysis. Default is FALSE

CDR_column

(Optional) cellular detection rate column name

plotWidth

User-defined plot width, Default 10 in

plotHeight

User-defined plot height, Default 10 in

fileName

User-defined file name, Default outputFile

filePATH

User-defined output directory PATH Default, current directory

Examples

## Not run: 
palmo_obj <- sclongitudinalDEG(ann=metadata, dataObj=pbmc, scassay="RNA",
group_column="celltype")

## End(Not run)

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