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fish4myeloma

Early development 2024, breaking changes likely Preliminary abnormality detection not yet finalised

fish4myeloma extracts Myeloma abnormalities from cytogenetic FISH (Fluorescence in situ hybridization) data represented in strings according to the ISCN standardised nomenclature.

Installation

You can install the development version of fish4myeloma from GitHub with:

# install.packages("devtools")
devtools::install_github("andysouth/fish4myeloma")

Example

detect abnormalities in simple test data

library(fish4myeloma)

## make some simple test data
fish_raw <- dplyr::tibble(test_id = c(1:5),
                          fishstring=c("17p13(TP53x3) CKS1Bx3",
                                       "17p13(TP53x2) CKS1Bx2",
                                       "17p13(TP53x1) CKS1Bx1 FGFR3 con IGH",
                                       "IGH con MAF",
                                       "CCND1 con IGH"
                          ))

fish_processed <- fish_raw |> fish4all("fishstring")

knitr::kable(fish_processed)
test_id fishstring cks1b_repeat cks1b_normality del17p_normality ighfgfr3_normality ighmaf_normality ighccnd1_normality
1 17p13(TP53x3) CKS1Bx3 3 abnormal NA NA NA NA
2 17p13(TP53x2) CKS1Bx2 2 normal normal NA NA NA
3 17p13(TP53x1) CKS1Bx1 FGFR3 con IGH 1 abnormal abnormal abnormal NA NA
4 IGH con MAF NA NA NA NA abnormal NA
5 CCND1 con IGH NA NA NA NA NA abnormal 
# old way calling functions individually

# fish_processed <- fish_raw |>
#    fish4cks1b("fishstring") |>
#    fish4del17p("fishstring") |>
#    fish4ighfgfr3("fishstring") |>
#    fish4ighmaf("fishstring") |>
#    fish4ighccnd1("fishstring")

map abnormalities to OMOP ids, one per abnormality

(omop ids not added yet, can have in a lookup table from name)

fish_omop <- fish_processed |> fish2omop() 
#> Joining with `by = join_by(abnormality)`

knitr::kable(fish_omop)
test_id fishstring abnormality value loinc_fish
1 17p13(TP53x3) CKS1Bx3 cks1b abnormal 81752-8
3 17p13(TP53x1) CKS1Bx1 FGFR3 con IGH cks1b abnormal 81752-8
3 17p13(TP53x1) CKS1Bx1 FGFR3 con IGH del17p abnormal 81746-0
3 17p13(TP53x1) CKS1Bx1 FGFR3 con IGH ighfgfr3 abnormal 72726-3
4 IGH con MAF ighmaf abnormal 77033-9
5 CCND1 con IGH ighccnd1 abnormal 77037-0