A function to read binary karyotype data, stored in LGF format in JSON files produced by the CytoGPS web site, into R for further analysis.
The name of the JSON file (or a character vector of
such file names) from which you want to extract and format
The specified directory/folder from which the user
wants to extract JSON files. If
A logical value; should the function keep you informed about what it is doing?
readLGF function reads and parses these JSON files and
converts them into an R data structure. The
raw component of
this structure contains binary matrices that can serve as input to the
Mercator package (see
unsupervised analyses. The
frequency component summarizes the
fraction of input karyotype-clones with each abnormality, and can be
visualized with other tools in the
A list containing five elements:
source: A character vector containing the names of the
JSON files from which data was read.
raw: A list of lists, one per JSON source file. Each
internal list contains two elements,
Status is a data frame with one row per
karyotype in the input file, describing the results of CytoGPS
parsing and mapping. Results can be "
Nonfixable grammar error",
Fixable grammar error and success", or
Fixable grammar error but containing validation error".
LGF is a data frame where the columns are LGF-cytobands and the
rows are clones from the successfully processed input karyotypes;
each karyotype can have multiple clones. Entries are zero or one
indicating the absence or presence of an abnormality.
frequency: A data frame, where the rows are cytobands
and the columns are Loss, Gain, and Fusion, with three columns per
input file. Entries are the fraction of karyotype clones with
size: An integer vector containing the total number of
clones per input file. These values can be used to turn fractions
back into counts.
CL: A data frame with one row per cytoband detailing
the chromosomal location and (grayscale) color of the band
produced by Giemsa staining.
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. Under review.
Abrams ZB, Tally DG, Coombes KR. RCytoGPS: An R Package for Analyzing and Visualizing Cytogenetic Data. In preparation.
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