genogamesh

installation

You can install the development version of genogamesh like so:

devtools::install_github("william-swl/genogamesh")

parse bioinfomatic data

• 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)

shortcuts for bioinfomatic pipelines

• 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)

IO

read_fasta()

write_fasta()

read_vcf()

read_gff()

S4 classes in genogamesh

mutstr

• 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