get_ordIndex: Perform reCAT

In tinglabs/reCAT: Reconstructing Cell Cycle Pseudo Time-Series via Single-Cell Transcriptome Data

Description

This function performs reCAT on your data, generating the order index of each cell as output.

Usage

get_ordIndex(
  test_exp,
  threadnum,
  step_size = 2,
  base_cycle_range = c(6:9),
  max_loop = NULL,
  clust_method = NULL
)

Arguments

test_exp	The gene expression input obtained from get_test_exp
threadnum	The number of threads to use
step_size	The interval of cycles to merge in the algorithm. Defaults to 2
base_cycle_range	Sets the cluster number used to formulate the base cycle, can be set as c(6:9) or c(7:10). Defaults to c(6:9)
max_loop	This sets the maximum number for not applying step_size in reCAT, i.e. if N = 100, step_size = 5, and max_loop = 50. Then reCAT merges consecutive cycles from 10 to 50, then merges cycles by intervals of 5 from 55 to 100.
clust_method	There are two clustering approaches: GMM ("GMM") and correlation-based ("Corr"). This defaults to NULL, where reCAT uses "GMM" for datasets with less than 300 cells and "Corr" for > 300. We recommend "GMM" for better accuracy but only for small datasets (as it fails to cluster on larger datasets), and "Corr" for efficiency and larger datasets.

Examples

get_ordIndex(data, threadnum = 2, step_size = 2, base_cycle_range = c(6:9))

tinglabs/reCAT documentation built on March 16, 2021, 12:08 a.m.