palmo-class: palmo class

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

palmo class

Description

This function creates PALMO class object. All the raw data and results from PALMO are stored in this object.

Value

PALMO S4 class

Fields

raw

list, contains user entered annotation and expression dataframe or object

curated

list, contains curated input data

result

list, output from PALMO stored in result list

nDonors

numeric, number of donors in the input data

rownames

character, row names of the expression data

colnames

character, column names of the expression data

housekeeping_genes

character, user-defined housekeeping genes listed

datatype

character, datatype used like bulk or singlecell

omics

character, omics such as RNA, scRNA, scATAC

featureSet

character, parameters used for variance analysis

meanThreshold

numeric, Average expression threshold

cvThreshold

numeric, CV threshold

median_cvThreshold

numeric, median of CV threshold (from inter-donor)

groupName

character, group defined by user like celltype, cluster

group_oi

character, selected types from user-defined group list

donorThreshold

numeric, minimum donors to explore

groupThreshold

numeric, minimum group types to explore

topFeatures

numeric, number of top features to retrieve

donor_sep

character, donor and group separator such as ':'

cor_method

character, correelation method 'pearson', 'spearman'

clusterBy

character, cluster by a group (celltype or cluster)

z_cutoff

numeric, z-cutoff value for outlier analysis

filePATH

character, PATH of outout directory

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