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