cal_CRDscore: Calculate Circadian rhythm disruption score using scRNA or...

In leihe2021/CRDscore: An R package for calculation of circadian rhythm disruption score (CRDscore)

Calculate Circadian rhythm disruption score using scRNA or bulk transcriptomic data

Description

Calculate Circadian rhythm disruption score using scRNA or bulk transcriptomic data

Usage

cal_CRDscore(
  expr,
  circadians = NULL,
  study.type = NULL,
  num.rounds = 1000,
  n.bins = 50,
  seed = TRUE
)

Arguments

expr	log2 transformed TPM matrix derived from scRNAseq, or normalized gene expression matrix from bulk samples; rows are genes, cols are cells or samples.
circadians	The character vectors containing selected circadian features.
study.type	A string value to indicate the study type for calculation. Allowed values contain c('scRNAseq', 'bulk_RNAseq').
num.rounds	A integer value to indicate the permutation times of iteration; 1000 by default and 10000 will be better for reproducibility.
n.bins	A integer value giving expression bins within genes, which were binned according to their average expression across cells or samples. Set to 50 by default.
seed	A logical value to indicate if set random seed for reproducible results. TRUE by default.

Value

Continuous numerical variables with CRDscore, named by cells or samples.

Author(s)

Leihe, Yixian Fan.

Examples

## Not run: 
data("exprset")
data("circadians_selected")
CRDscore <- cal_CRDscore(expr = exprset, circadians = circadians_selected, study.type = "scRNAseq")

## End(Not run)

leihe2021/CRDscore documentation built on April 22, 2022, 8:45 p.m.