PALMO (version 0.1.2)

outlierDetect: 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
)

Value

PALMO object with outlier_res dataframe

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

Examples

if (FALSE) {
palmo_obj <- outlierDetect(data_object=palmo_obj, z_cutoff=2)
}