These data sets contain binary versions of subsets of cytogenetic karyotype data from patients with chronic myelogenous leukemia (CML).
data("lgfFeatures")
data("CML500")
data("CML1000")
data("fakedata") # includes "fakeclin"lgfFeaturesA data matrix with 2748 rows and 6 columns
listing the cytogentic bands produced as output of the CytoGPS
algorithm that converts text-based karyotypes into a binary
Loss-Gain-Fusion (LGF) model. The columns include the Label
(the Type and Band, joined by an underscore),
Type (Loss, Gain, or Fusion), Band (standard name of
the cytogenetic band), Chr (chromosome), Arm (the
chromsome arm, of the form #p or #q), and Index (an integer
that can be used for sorting or indexing).
CML500A BinaryMatrix object with 770
rows (subset of LGF features) and 511 columns (patients). The
patients were selected using the downsample function
from the full set of more than 3000 CML karyotypes. The rows were
selected by removing redundant and non-informative features when
considering the full data set.
CML1000A BinaryMatrix object with 770
rows (subset of LGF features) and 1057 columns (patients). The
patients were selected using the downsample function
from the full set of more than 3000 CML karyotypes. The rows were
selected by removing redundant and non-informative features when
considering the full data set.
fakedataA matrix with 776 rows ("features") and 300 columns ("samples") containng synthetic continuos data.
fakeclinA data frame with 300 rows ("samples") and 4
columns of synthetic clincal data related to the fakedata.
Kevin R. Coombes <krc@silicovore.com>, Caitlin E. Coombes
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 Jul 2. pii: btz520. doi: 10.1093/bioinformatics/btz520. [Epub ahead of print]