sc_mutations {FLAMES} | R Documentation |
Candidate SNVs identified with filtering by coverage threshold, and allele frequency range.
sc_mutations( sce, barcode_tsv, bam_short, out_dir, genome_fa, annot, known_positions = NULL, min_cov = 100, report_pct = c(0.1, 0.9) )
sce |
The |
barcode_tsv |
TSV file for cell barcodes |
bam_short |
(Optional) short read alignment BAM file. If provided, it is used to filter the variations. Variations in long-read data with enough short read coverage but no alternative allele will not be reported. |
out_dir |
(Optional) Output folder of sc_long_pipeline. Output files from this function will also be saved here.
Use this parameter if you do not have the |
genome_fa |
(Optional) Reference genome FASTA file. Use this parameter is if you do not wish |
annot |
(Optional) The file path to gene annotation file in gff3 format. If provided as |
known_positions |
(Optional) A list of known positions, with by chromosome name followed by the position, e.g. ('chr1', 123, 'chr1', 124, 'chrX', 567). These locations will not be filtered and its allele frequencies will be reported. |
min_cov |
The coverage threshold for filtering candidate SNVs. Positions with reads less then this number will not be considered. |
report_pct |
The allele frequency range for filtering candidate SNVs. Positions with less or higher allele frequency will not be reported. The default is 0.10-0.90 |
Takes the SingleCellExperiment
object from sc_long_pipeline
and the cell barcodes as barcode
.
Alternatively, input can also be provided as out_dir
, genome_fa
, annot
, barcode
.
a data.frame
containing the following columns:
chr - the chromosome where the mutation is located
position
REF - the reference allele
ALT - the alternative allele
REF_frequency - reference allele frequency
REF_frequency_in_short_reads - reference allele frequency in short reads (-1 when short reads not provided)
hypergeom_test_p_value
sequence_entropy
INDEL_frequency
adj_p - the adjusted p-value (by Benjamini–Hochberg correction)
The table is sorted by decreasing adjusted P value.
files saved to out_dir/mutation:
ref_cnt.csv.gz
alt_cnt.csv.gz
allele_stat.csv.gz
freq_summary.csv