sclongitudinalDEG: sclongitudinalDEG Function

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

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)

PALMO documentation built on Aug. 18, 2022, 1:06 a.m.