R package for querying 10x WGS and single-cell BAMs
devtools::install_github('mskilab/gUtils')
devtools::install_github('mskilab/bamUtils')
Instantiate a bambi object:
Methods:
-
grab_bx()
grab_bx(barcodes, query=NULL, data.table = FALSE, verbose = FALSE, mc.cores = 1)
-
grab_cb()
grab_cb(barcodes, query=NULL, data.table = FALSE, verbose = FALSE, mc.cores = 1)
-
grab_ub()
grab_ub(barcodes, query=NULL, data.table = FALSE, verbose = FALSE, mc.cores = 1)
-
fetch_by_tag()
fetch_by_tag(tag, tag_queries, query=NULL, data.table = FALSE, verbose = FALSE, mc.cores = 1)
- Instantiate a
bambiobject
library(bambi)
> hcc1143_subset = bambi$new(bam_file = "subsetHCC1143_phased_possorted0001.bam", bamdb_path="subsetHCC1143_phased_possorted0001_lmdb")
- Call methods
> hcc1143_subset$grab_bx('CGACGTGTCCTCTAGC-1')
GRanges object with 2 ranges and 11 metadata columns:
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [147975454, 147975580] + |
[2] chr1 [147975675, 147975824] - |
qname flag mapq cigar
<character> <numeric> <numeric> <character>
[1] ST-K00126:3:H5TL3BBXX:2:2109:25926:37800 99 16 127M
[2] ST-K00126:3:H5TL3BBXX:2:2109:25926:37800 147 16 150M
rnext pnext tlen
<character> <numeric> <numeric>
[1] = 147975676 371
[2] = 147975455 -371
seq
<character>
[1] ATGTCTTCTTCCTCATTATCTGGCACTGGTTAGGAAGCACTCATCTCCATGAAGTCATCTTTTGTTAATTCCTCTGGTGTGGTGTGTATTAGCTCTTAAATTCCTCCAAGATCCATATCTTGCAACC
[2] ATCTGGACACAAATTGTACTTTTGTCCAGCACGAATTTATTGTTTTGAGTTTCATGGTTTTCTATATCAACTGATGACATCTTGAAAGGTGTAAGCCTTCCAGACTTCCATGATGTTCTCTCTATTGGGTTTCTCTTTTGCAATGTTGAC
qual
<character>
[1] JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJAJFJJJJJJJJJFJJJJJJJJJJFJJJJFFFJJJFJJJJJJAAJFJJJFAFAFFFJAA<7F<
[2] A<7FFFJFFFAJJAAAJJF<F<7A-<AA-<<<AFFJJJJJJJJFFJAFFAAFJFJJJAFFJJJJJJJJJJFJFAJJJJJJFJJJJJJ<FFJJJFJJJFJJJJJJJJJJJJJFJJJJFFJ7JJJJF<JJJJJJJJJJJJJJJJJJJFFAA<
BX qwidth
<character> <integer>
[1] CGACGTGTCCTCTAGC-1 127
[2] CGACGTGTCCTCTAGC-1 150
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths