ti_raceid_stemid.RdWill generate a trajectory using RaceID / StemID.
This method was wrapped inside a container. The original code of this method is available here.
ti_raceid_stemid(knn = 10L, ccor = 0.4, metric = "pearson", sat = TRUE, samp = 1000L, cln = 30L, clustnr = 30L, bootnr = 50L, FUNcluster = "kmedoids", probthr = 0.001, outminc = 5L, outlg = 2L, outdistquant = 0.95, initial_cmd = TRUE, perplexity = 30L, cthr = 5L, nmode = TRUE, projcells_knn = 3L, fr = FALSE, pdishuf = 500L, fast = FALSE, pthr = 0.01, scthr = 0.2)
| knn | Number of nearest neighbors used to infer corresponding cell types in different batches. Domain: U(5, 50). Default: 10. Format: integer. |
|---|---|
| ccor | Correlation coefficient used as a treshhold for determining genes correlated to eachother. Domain: U(0, 1). Default: 0.4. Format: numeric. |
| metric | Distances are computed from the filtered expression matrix after optional feature selection, dimensional reduction, and/or transformation (batch correction). Domain: pearson, spearman, logpearson, euclidean. Default: pearson. Format: character. |
| sat | If |
| samp | Number of bootstrapping runs for clusterboot. Domain: e^U(3.91, 9.21). Default: 1000. Format: integer. |
| cln | Number of clusters to be used. If |
| clustnr | Maximum number of clusters for the derivation of the cluster number by the saturation of mean within-cluster-dispersion. Domain: U(10, 100). Default: 30. Format: integer. |
| bootnr | Number of booststrapping runs for clusterboot. Domain: U(20, 100). Default: 50. Format: integer. |
| FUNcluster | Clustering method used by RaceID3. Domain: kmedoids, kmeans, hclust. Default: kmedoids. Format: character. |
| probthr | Outlier probability threshold for a minimum of outlg genes to be an outlier cell. This probability is computed from a negative binomial background model of expression in a cluster. Domain: e^U(-11.51, 0.00). Default: 0.001. Format: numeric. |
| outminc | Minimal transcript count of a gene in a clusters to be tested for being an outlier gene. Domain: U(0, 100). Default: 5. Format: integer. |
| outlg | Minimum number of outlier genes required for being an outlier cell. Domain: U(0, 100). Default: 2. Format: integer. |
| outdistquant | Real number between zero and one. Outlier cells are merged to outlier clusters if their distance smaller than the outdistquant-quantile of the distance distribution of pairs of cells in the orginal clusters after outlier removal. Domain: U(0, 1). Default: 0.95. Format: numeric. |
| initial_cmd | If TRUE, then the t-SNE map computation is initialized with a configuration obtained by classical multidimensional scaling. Default: TRUE. Format: logical. |
| perplexity | Perplexity of the t-SNE map. Domain: U(5, 100). Default: 30. Format: integer. |
| cthr | Clusters to be included into the StemID2 analysis must contain more than cthr cells. D. Domain: U(1, 25). Default: 5. Format: integer. |
| nmode | If |
| projcells_knn | See |
| fr | Use Fruchterman-Rheingold layout instead of t-SNE for dimensional-reduction representation of the lineage tree. Default: FALSE. Format: logical. |
| pdishuf | Number of randomizations of cell positions for which to compute projections of cells on inter-cluster links. Domain: e^U(2.30, 9.21). Default: 500. Format: integer. |
| fast | If |
| pthr | P-value cutoff for link significance. This threshold is applied for the calculation of link scores reflecting how uniformly a link is occupied by cells. Domain: e^U(-11.51, 0.00). Default: 0.01. Format: numeric. |
| scthr | Score threshold for links to be shown in the graph. Domain: U(0, 1). Default: 0.2. Format: numeric. |
A TI method wrapper to be used together with
infer_trajectory
Grün, D., Muraro, M.J., Boisset, J.-C., Wiebrands, K., Lyubimova, A., Dharmadhikari, G., van den Born, M., van Es, J., Jansen, E., Clevers, H., de Koning, E.J.P., van Oudenaarden, A., 2016. De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data. Cell Stem Cell 19, 266–277.