Description Usage Arguments Value
Generate Alleloscope object for analysis
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alt_all |
A SNP by cell read count matrix/ spare matrix for the alternative alleles. |
ref_all |
A SNP by cell read count matrix/ spare matrix for the reference alleles. |
samplename |
Sample name for the data. |
genome_assembly |
The genome assembly used for sequencing alignment. (ex: "GRCh38" or "GRCh37") |
dir_path |
Path of the output directory. |
barcodes |
A matrix/ data.frame with barcodes for each cell in the first column. |
size |
A matrix with two columns: col1: different chromosome; col2: for the size (bp) of different chromosomes. |
assay |
A character indicating the type of sequencing data. (ex: "scDNAseq" or "scATACseq") |
cov |
Logical (TRUE/FALSE). Whether or not to use only coverage. If "cov" is TRUE, alt_all, ref_all, andvcf_all are not required. |
vcf_all |
A matrix/ data.frame of the vcf format for SNP information. (The length and order are the same as nrow(alt_all) and nrow(alt_all)) |
A Alleloscope object including the necessary information.
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