ti_oscope: Oscope

In dynverse/dynmethods: A collection of trajectory inference methods

Oscope

Description

Will generate a trajectory using Oscope.

This method was wrapped inside a container. The original code of this method is available here.

Usage

ti_oscope(
  alternative_median = FALSE,
  filter_genes = TRUE,
  mean_cut = c(100L, 100000000L),
  qt = c(0.05, 0.95),
  quan = 0.95,
  ndg = 3L,
  nchun = 4L,
  niter = 20000L,
  ncthre = 1000L
)

Arguments

alternative_median	If alternative = TRUE, the alternative version of median normalization will be applied.The alternative method is similar to median-by-ratio normalization, but can deal withthe cases when all of the genes/isoforms have at least one zero counts (in which casethe median-by-ratio normalization will fail). Default: FALSE. Format: logical.
filter_genes	Whether or not to filter the genes using the CalcMV function. Default: TRUE. Format: logical.
mean_cut	It is suggested to apply Oscope on genes with high mean and high variance.By default, the lower boundary is specified as 100, consequently only geneswith mean > 100 will be used. The CalcMV function will fit a linear regressionon log(variance)~log(mean) on these genes. Genes with variance above thisline are considered as the high mean high variance genes. Domain: ( e^U(2.30, 4.61), e^U(4.61, 18.42) ). Default: (100, 100000000). Format: integer_range.
qt	Thresholds for outlier adjustment. For each gene/isoform, values <= qt1 thquantile (>= qt2 th quantile) will be pushed to qt1 th quantile (qt2 th quantile)prior to the scaling. default values are 0.05 and 0.95. Domain: ( U(0, 1), U(0, 1) ). Default: (0.05, 0.95). Format: numeric_range.
quan	Only gene pairs with similarity score >= quan th quantile will be considered in the clustering analyses. Domain: U(0, 1). Default: 0.95. Format: numeric.
ndg	Degree of polynomial. Domain: U(1, 10). Default: 3. Format: integer.
nchun	Number of starting points for polynomial fitting. Domain: U(1, 10). Default: 4. Format: integer.
niter	The 2-opt algorithm will stop if N iterations has been performed or if the optimal order. Domain: e^U(6.91, 13.82). Default: 20000. Format: integer.
ncthre	No description was found. Domain: e^U(4.61, 11.51). Default: 1000. Format: integer.

Value

A TI method wrapper to be used together with infer_trajectory

References

Leng, N., Chu, L.-F., Barry, C., Li, Y., Choi, J., Li, X., Jiang, P., Stewart, R.M., Thomson, J.A., Kendziorski, C., 2015. Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nature Methods 12, 947–950.

dynverse/dynmethods documentation built on Jan. 18, 2024, 4:44 a.m.