pc_as_pt: Take a principal component (first by default) and return a...
In maehrlab/thymusatlastools: Tools for analysis of single-cell transcriptomic data
Description
Usage
Arguments
Value
Description
Take a principal component (first by default) and return a list of results gained by interpreting that PC as a pseudotime axis.
Usage
1
pc_as_pt(dge, pc.use = 1, orient_var = "eday")
Arguments
dge:
Seurat object to be used. Should have variable genes and PCA fields already filled in.
Jackstraw and t-SNE are optional but preferred.
orient_var:
pseudotime is flipped to correlate positively with this. Anything available
from ‘Seurat::FetchData(dge, orient_var)' is fair game... as long as it’s numeric.
pc.use:
which principal component to take
Value
List with named elements:
'$dge': Seurat object with a 'pseudotime' metadatum filled in
'$gene_corrs': dataframe with genes ordered by correlation with pseudotime.
Columns are 'gene', 'corr', and (if available from Jackstraw) 'p_value'.
maehrlab/thymusatlastools documentation built on May 28, 2019, 2:32 a.m.
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Description Usage Arguments Value
Description
Take a principal component (first by default) and return a list of results gained by interpreting that PC as a pseudotime axis.
Usage
1 | pc_as_pt(dge, pc.use = 1, orient_var = "eday")
|
Arguments
dge: |
Seurat object to be used. Should have variable genes and PCA fields already filled in. Jackstraw and t-SNE are optional but preferred. |
orient_var: |
pseudotime is flipped to correlate positively with this. Anything available from ‘Seurat::FetchData(dge, orient_var)' is fair game... as long as it’s numeric. |
pc.use: |
which principal component to take |
Value
List with named elements: '$dge': Seurat object with a 'pseudotime' metadatum filled in '$gene_corrs': dataframe with genes ordered by correlation with pseudotime. Columns are 'gene', 'corr', and (if available from Jackstraw) 'p_value'.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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