get_phase_score: Assign phase score

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

To calculate the phase score, Macosko (2015) used mean expression of genes that mark a particular phase of the cell cycle. Not all genes in the list are used. Only those that correlate with the mean expression are included, followed by some normalisation. I am not certain whether to apply normalisation or not, given that this research uses batch combined data that has already been normalised. Qualitatively in a heatmap, the results did not look much different.

Usage

get_phase_score(
  x,
  gene_vec = NULL,
  norm_factor = F,
  norm_column = F,
  norm_row = F
)

Arguments

x	an expression matrix
gene_vec	a vector of genes with their names being which cell cycles they are expressed

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.