Type: Package
Title: Data for Package 'Qindex'
Version: 0.1.3
Date: 2025-01-18
Description: Example data used in package 'Qindex'.
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.3.2
Encoding: UTF-8
License: GPL-2
Depends: R (≥ 4.3),
Language: en-US
Suggests: knitr
NeedsCompilation: no
Packaged: 2025-01-18 14:54:17 UTC; tingtingzhan
Author: Tingting Zhan ORCID iD [aut, cre, cph], Misung Yi ORCID iD [aut, cph], Inna Chervoneva ORCID iD [aut, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-18 22:10:05 UTC

Data for Package 'Qindex'

Description

Example data used in package 'Qindex'.

Author(s)

Maintainer: Tingting Zhan tingtingzhan@gmail.com (ORCID) [copyright holder]

Authors:

References

Selection of optimal quantile protein biomarkers based on cell-level immunohistochemistry data. Misung Yi, Tingting Zhan, Amy P. Peck, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, Hai Hu, Yunguang Sun, Hallgeir Rui and Inna Chervoneva. BMC Bioinformatics, 2023. doi:10.1186/s12859-023-05408-8

Quantile index biomarkers based on single-cell expression data. Misung Yi, Tingting Zhan, Amy P. Peck, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, Hai Hu, Yunguang Sun, Hallgeir Rui and Inna Chervoneva. Laboratory Investigation, 2023. doi:10.1016/j.labinv.2023.100158

Ki67 Data

Description

Ki67 cell data containing 622 patients

Usage

Ki67

Format

PATIENT_ID

factor, unique patient identifier

tissueID

factor, TMA core identifier

RECURRENCE

integer, recurrence indicator, 1 = Recurred, 0 = not Recurred

RECFREESURV_MO

integer, recurrence-free survival time in months

Marker

double, cell signal intensity of the protein immunofloerscence signal

inner_x

integer, x-coordinate in the cell centroid in the TMA core

inner_y

integer, y-coordinate in the cell centroid in the TMA core

AGE_AT_DX

integer, age at diagnosis

Tstage

integer, tumor stage

NodeSt

integer, node stage, -1 = unknown, 0 = Node Negative, 1 = Node Positive

HRpos

integer, indicator of hormone positive status (ER+ or PR+), 1 = positive, 0 = negative

HistologicalGrade

integer, histology grade

Her2_path_qIF

integer, Her2 status, 1 = positive, 0 = negative

RACE

character, race, White, Black, Asian, Native Hawaiian or Other Pacific Islander, American Indian or Alaska Native, Unknown

RadjCHEMO

integer, adjuvant chemo treatment, 0 = unknown, 1 = done, 2 = NOT done

RadjRAD

integer, adjuvant radiation treatment, 0 = unknown, 1 = done, 2 = NOT done

HORM_4cat

integer, hormone treatment, 0 = unknown, 1 = not indicated, 2 = done, 3 = recommended, but not done

MSI

double, mean signal intensity (mean over all cells in the TMA core)