Description Usage Arguments Value Examples
LoadAnnovar
loads Annovar data for the provided cell to file mapping.
By default, does not perfom any quality control on variant call files.
LoadAnnovar
should be provided *.variant_function
files
for each cell. If additional exonic functional pruning is required,
LoadAnnovar
will automatically extract the location of the corresponding
*.exonic_variant_function
file locally.
1 2 3 4 | LoadAnnovar(cells, annovar.filenames, germline.filename,
reduction = "by_gene", somatic.only = TRUE, exonic.only = TRUE,
read.depth.norm.col = 10, spike.in.regex = "^ERCC-",
unique.id.cols = c(3, 4, 5, 6, 7))
|
cells |
character vector containing cell IDs |
annovar.filenames |
character vector containing annovar file paths. |
germline.filename |
file path for annovar file containing germline variants. Used as a positive control for single-cell somatic variant analysis. |
reduction |
reduction to use from annovar to Seurat assay. Currently 'by_gene' |
somatic.only |
boolean, default TRUE, produce counts based only on predicted somatic variants (subtact germline) |
exonic.only |
boolean, default TRUE, produce counts based only on variants predicted to occur within exons. |
read.depth.norm.col |
default 10, col with read depth to normalize variant calls by for single cell analysis. If using the default Annovar conversion tools from VCF, this will most likely be column 10. |
spike.in.regex |
regex selection for 'CHR' vcf field inidcating synthetic spike-in. Used as a negative control for single-cell somatic variant analysis. Default '^ERCC-' |
unique.id.cols |
set of columns that uniquely define a variant in the *.variant_function file. Will be used to generate row names for the final aggregated data set. |
A matrix containing the reduced counts of each ENSG merged from all cells supplied in a Seurat-importable format.
1 2 3 4 5 6 7 8 | ## Not run:
LoadAnnovar(c('1', '2'),
c('1.anno.variant_function', '2.anno.variant_function')
)
## End(Not run)
|
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