outlierDetect: outlierDetect Function

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

outlierDetect Function

Description

This function allows users to perform outlier analysis on bulk data by calculating z-score. Outlier genes defined as mean/SD = |Z| > z_cutoff.

Usage

outlierDetect(
  data_object,
  z_cutoff = NULL,
  plotWidth = 10,
  plotHeight = 5,
  group_column = NULL,
  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.
z_cutoff	|Z| cutoff threshold to find potential outliers (Eg. z_cutoff=2, equals to Mean/SD 2)
plotWidth	User-defined plot width, Default 10 in
plotHeight	User-defined plot height, Default 5 in
group_column	Include group by outlier analysis (celltype, cluster)
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

PALMO object with outlier_res dataframe

Examples

## Not run: 
palmo_obj <- outlierDetect(data_object=palmo_obj, z_cutoff=2)

## End(Not run)

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