RCytoGPS (version 1.2.10)

preclean: Pre-clean Karyotypes

Description

A function to clean karyotype data, by deleting known comments that do not adhere to the ISCN standard.

Usage

preclean(x, targetColumns, dirt)

Value

A data frame of te same size and with the same number of columns as the input data frame.

Arguments

x

A data frame containing at least one column of karyotype data.

targetColumns

Either a numeric vector of column indices or a character vector of column names.

dirt

A character vector containing items to delete from all karyotypes,

Author

Kevin R. Coombes

Details

The core input data worked on by the RCytoGPS are karyotypes, which are text strings written to conform to the ISCN standard. At many institutions, the cytogeneticists have developed idiosyncratic conventions that they use to add comments into the string. In most cases, these karyotypes are simply stored as text strings in a local database. In particular, they are not checked for synatx or grammar errors. By contrast, the implementation of the CytoGPS algorithm at the web site http://cytogps.org uses a formal approach with lexer and parser. As a result, many karyotypes are rejected by the system.

The preclean function uses gsub to delete a list of known (local) comments from all karyotypes, making it more likley that they will be successfully processed by the lexer and parser. We provide an example list derived from experience at our own institution.

Implementation Note: The preclean function removes strings in the order that they are contained in the dirt vector. So, you have to be carefully not to delete parts of a long phrase before trying to delete the whole phrase. For example, you should not remove "clonal" before removing "nonclonal".

References

Abrams ZB, Zhang L, Abruzzo LV, Heerema NA, Li S, Dillon T, Rodriguez R, Coombes KR, Payne PRO. CytoGPS: a web-enabled karyotype analysis tool for cytogenetics. Bioinformatics. 2019 Dec 15;35(24):5365-5366.

Abrams ZB, Tally DG, Zhang L, Coombes CE, Payne PRO, Abruzzo LV, Coombes KR. Pattern recognition in lymphoid malignancies using CytoGPS and Mercator. In Press.

Abrams ZB, Tally DG, Coombes KR. RCytoGPS: An R Package for Analyzing and Visualizing Cytogenetic Data. In preparation.

Examples

cleanDir <- system.file("PreClean", package = "RCytoGPS")
bad <- read.delim(file.path(cleanDir, "badStrings.txt"), header=FALSE)
bad <- as.vector(as.matrix(bad))
input <- read.csv(file.path(cleanDir, "startKaryotypes.csv"))
myclean <- preclean(input, 4:5, bad)