get_start: Determining the starting cell

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

Description

This function is used to find the starting cell of the cycle

Usage

get_start(
  bayes_score,
  mean_score,
  ordIndex,
  cls_num,
  rdata = NULL,
  nthread = 3
)

Arguments

bayes_score	Obtained from get_score function
mean_score	Obtained from get_score function
ordIndex	Obtained from get_ordIndex function
cls_num	The number of cell cycle stages that you want to segment, ie 3 - G1, S, G2/M.
rdata	This sets the region of each cycle stage manually by observing the scores. Usage: rdata = t(data.frame(c(2,5), c(10,15), c(20,25))) corresponding to G1: 2-5, S: 10-15 and G2/M: 20-25. If NULL, it will prompt you to enter the region values such as '2 5', please enter twice to confirm each line of input.
nthreads	The number of threads. Defaults to 3

Examples

test_exp <- get_test_exp(data)
data_ordIndex <- get_ordIndex(test_exp, 2)
score_results <- get_score(t(test_exp))
rdata = t(data.frame(c(2,5), c(10,15), c(20,25)))
data_start <- get_start(score_results$bayes_score, score_results$mean_score, data_ordIndex, cls_num = 3, rdata,  nthread = 3)

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