You can install the development version of genogamesh like so:
devtools::install_github("william-swl/genogamesh")- parse the output of SingleR
# SingleR(test, ref) %>% parse_SingleR()- parse somatic hypermutation from igblast output
# parse_IgBlast_shm('igblast_out.txt')- parse sequences from CellRanger vdj output
# parse_CellRanger_vdjseq(df)
# parse_CellRanger_vdjseq(df, file='seq.csv')
# parse_CellRanger_vdjseq(df, file='seq.fa', fa_content='seq_orf_nt')- parse sequences from ANARCI vdj output
# parse_ANARCI_aaseq(df, chain='H')
# parse_ANARCI_aaseq(df, chain='L')
# keep the ab numbering
# parse_ANARCI_aaseq(df, chain='H', keep_number=TRUE)- parse vcf file with the help of reference genome and annotations. It is still under development, which can not process more than 3 nt substitutions in a single record row of vcf file, and can not process indels
# vcf <- read_vcf(...)
# fa <- read_fasta(..)
# gff <- read_gff(...)
# parse_vcf(vcf, fa, gff)- add SingleR celltype annotation for Seurat object
# SE <- SingleR_SE(SE, SEref)- reduction from raw Seurat object created by read count matrix, including normalization, variable features calling, scaling, PCA and UMAP
# SE <- reduction_SE(SE)- translate nucleotides into amino acids from the first character
nt2aa(c("ATGAAA", "TTGCCC", "CTGTTT"))
#> [1] "MK" "LP" "LF"- build antigen map from sera titer data
# antigen_map(data, sera_meta, ag_meta, seed=14)read_fasta()
write_fasta()
read_vcf()
read_gff()
- a S4 class to manipulate mutation strings
- support set operations
raw_mut_string <- c(
variant1 = "T10I,D20N,Q30E,A40T,P50L,G60R",
variant2 = "T10I,D20-,Q30E,A40T,P50L,G60R,S80R",
variant3 = "T10A,D20G,Q30E,A40T,P50L,G60R"
)
m <- mutstr(raw_mut_string, sep = ",")
m
#> mutstr 3
#> @ names: variant1 variant2 variant3
#> @ sep: ,
#> @ mstr:
#> [1] T10I,D20N,Q30E,A40T,P50L,G60R
#> [2] T10I,D20-,Q30E,A40T,P50L,G60R,S80R
#> [3] T10A,D20G,Q30E,A40T,P50L,G60R
#> @ mut:
#> [1] T10I D20N Q30E A40T P50L G60R
#> [2] T10I D20- Q30E A40T P50L G60R S80R
#> [3] T10A D20G Q30E A40T P50L G60R
names(m)
#> [1] "variant1" "variant2" "variant3"
mstr(m)
#> variant1 variant2
#> "T10I,D20N,Q30E,A40T,P50L,G60R" "T10I,D20-,Q30E,A40T,P50L,G60R,S80R"
#> variant3
#> "T10A,D20G,Q30E,A40T,P50L,G60R"
mut(m)
#> $variant1
#> [1] "T10I" "D20N" "Q30E" "A40T" "P50L" "G60R"
#>
#> $variant2
#> [1] "T10I" "D20-" "Q30E" "A40T" "P50L" "G60R" "S80R"
#>
#> $variant3
#> [1] "T10A" "D20G" "Q30E" "A40T" "P50L" "G60R"
m[1:2]
#> mutstr 2
#> @ names: variant1 variant2
#> @ sep: ,
#> @ mstr:
#> [1] T10I,D20N,Q30E,A40T,P50L,G60R
#> [2] T10I,D20-,Q30E,A40T,P50L,G60R,S80R
#> @ mut:
#> [1] T10I D20N Q30E A40T P50L G60R
#> [2] T10I D20- Q30E A40T P50L G60R S80R
m[[2]]
#> [1] "T10I" "D20-" "Q30E" "A40T" "P50L" "G60R" "S80R"
intersect(m, m[1])
#> mutstr 3
#> @ names: variant1 variant2 variant3
#> @ sep: ,
#> @ mstr:
#> [1] T10I,D20N,Q30E,A40T,P50L,G60R
#> [2] T10I,Q30E,A40T,P50L,G60R
#> [3] Q30E,A40T,P50L,G60R
#> @ mut:
#> [1] T10I D20N Q30E A40T P50L G60R
#> [2] T10I Q30E A40T P50L G60R
#> [3] Q30E A40T P50L G60R
setdiff(m, m[1])
#> mutstr 3
#> @ names: variant1 variant2 variant3
#> @ sep: ,
#> @ mstr:
#> [1]
#> [2] D20-,S80R
#> [3] T10A,D20G
#> @ mut:
#> [1]
#> [2] D20- S80R
#> [3] T10A D20G
union(m, m[1])
#> mutstr 3
#> @ names: variant1 variant2 variant3
#> @ sep: ,
#> @ mstr:
#> [1] T10I,D20N,Q30E,A40T,P50L,G60R
#> [2] T10I,D20-,Q30E,A40T,P50L,G60R,S80R,D20N
#> [3] T10A,D20G,Q30E,A40T,P50L,G60R,T10I,D20N
#> @ mut:
#> [1] T10I D20N Q30E A40T P50L G60R
#> [2] T10I D20- Q30E A40T P50L G60R S80R D20N
#> [3] T10A D20G Q30E A40T P50L G60R T10I D20N