Prep rna snps and create DNA & RNA snps (snpsGeno2) and RNA snps (snpsCalled)
make_snpsRNA(genotyped, called)| genotyped | CollapsedVCF containing snp info for genotype data |
|---|---|
| called | CollapsedVCF containing filtered snp info for rna data (generated by filtered_called) |
Named list containing snpsGeno2 and snpsCalled, both representing snp arrays as integers.
snpsCalled_filter <- filter_called(snpsCalled_VCF)
snpsRNA <- make_snpsRNA(snpsGeno_VCF, snpsCalled_filter)
#> # matching snps: 255
snpsRNA$snpsGeno2[1:5, 1:5]
#> 4463344375_R01C01 4463344375_R01C02 4572348848_R01C02
#> chr1:15660052_T/C 0 0 0
#> chr1:33772682_T/C 1 1 0
#> chr1:46027788_T/G 2 1 1
#> chr1:54653842_T/G 0 1 0
#> chr1:58682254_T/C 2 2 1
#> 4572348855_R01C02 5535549043_R01C01
#> chr1:15660052_T/C 1 0
#> chr1:33772682_T/C 1 0
#> chr1:46027788_T/G 1 0
#> chr1:54653842_T/G 1 1
#> chr1:58682254_T/C 1 1
snpsRNA$snpsCalled[1:5, 1:5]
#> R14030_H7K5NBBXX_accepted_hits.sorted.bam
#> chr1:15660052_T/C 0
#> chr1:33772682_T/C 1
#> chr1:46027788_T/G 2
#> chr1:54653842_T/G 2
#> chr1:58682254_T/C 1
#> R14184_H7K5NBBXX_accepted_hits.sorted.bam
#> chr1:15660052_T/C 2
#> chr1:33772682_T/C 0
#> chr1:46027788_T/G 0
#> chr1:54653842_T/G 1
#> chr1:58682254_T/C 2
#> R13904_H7K5NBBXX_accepted_hits.sorted.bam
#> chr1:15660052_T/C 0
#> chr1:33772682_T/C 0
#> chr1:46027788_T/G 1
#> chr1:54653842_T/G 1
#> chr1:58682254_T/C 1
#> R14296_H7JLCBBXX_accepted_hits.sorted.bam
#> chr1:15660052_T/C 0
#> chr1:33772682_T/C 0
#> chr1:46027788_T/G 1
#> chr1:54653842_T/G 1
#> chr1:58682254_T/C 0
#> R14247_HF3JYBBXX_accepted_hits.sorted.bam
#> chr1:15660052_T/C 0
#> chr1:33772682_T/C 0
#> chr1:46027788_T/G 1
#> chr1:54653842_T/G 0
#> chr1:58682254_T/C 2