Package 'ProliferativeIndex'

A function for calculating proliferative index from variance stabalized RNA-seq data in the ProliferativeIndex package

Description

This function allows the user to read in data for subsequent proliferative index calculation and analysis

Usage

calculatePI(userObject)

Arguments

userObject

Output from ProliferativeIndex readDataForPI function

Examples

calculatePI(exReadDataObj)

---

A function for comparing proliferative indices from variance stabalized RNA-seq data to model principal componenets in the ProliferativeIndex package

Description

This function allows the user to calculate a correlation between their model and PI

Usage

compareModeltoPI(userObject, vstPI)

Arguments

userObject	Output from ProliferativeIndex readDataForPI function (user data)
vstPI	Output from ProliferativeIndex calculatePI function

Examples

compareModeltoPI(exReadDataObj, exVSTPI)

---

A function for comparing proliferative indices from variance stabalized RNA-seq data in the ProliferativeIndex package

Description

This function allows the user to examine a summary and plot of their PIs

Usage

comparePI(vstPIinput)

Arguments

vstPIinput

Output from ProliferativeIndex calculatePI function (PI of user vst data)////////////////////////////////////////////////////////////////////////

Examples

comparePI(exVSTPI)

---

TCGA ACC data set output from readDataForPI function

Description

This object is the output from readDataForPI taking vstTCGA_ACCData_sub and this model: c("AIFM3", "ATP9B", "CTRC", "MCL1", "MGAT4B", "ODF2L", "SNORA65", "TPPP2")) as inputs.

Usage

data(exReadDataObj)

Format

A list of the vstData (vstTCGA_ACCData_sub data frame with 20501 rows and 10 columns) and the modelIDs (character vector of "AIFM3", "ATP9B", "CTRC", "MCL1", "MGAT4B", "ODF2L", "SNORA65", "TPPP2")

---

TCGA ACC data set output from calculatePI function

Description

This object is the output from calculatePI from the exReadDataObj as input.

Usage

data(exVSTPI)

Format

A numeric vector of the calculated Proliferation Indices for the vstTCGA_ACCData_sub data

---

A function for reading data in for use with the ProliferativeIndex package

Description

This function allows the user to read in variance stabalized RNA-seq data and gene model names for subsequent proliferative index calculation and analysis

Usage

readDataForPI(vstData, modelIDs)

Arguments

vstData	Dataframe of user variance stabalized count data (from DESeq2) with samples in columns and genes in rows. Rownames must be genes.
modelIDs	Genes in user identified model for comparison to proliferative index

Examples

readDataForPI(vstTCGA_ACCData_sub, c("AIFM3", "ATP9B", "CTRC", "MCL1", 
"MGAT4B", "ODF2L", "SNORA65", "TPPP2"))

---

TCGA ACC data set

Description

A dataset containing data from the The Cancer Genome Atlas (TCGA) Adrenocortical Carcinoma (ACC) dataset. This data was obtained from the TCGA data portal (tcga-data.nci.nih.gov) in June 2015. Level 3 RNASeqV2 raw count data was variance stabalized with the DESeq2 v1.8.2 varianceStabilizingTransformation:

Usage

data(vstTCGA_ACCData_sub)

Format

A data frame with 20501 rows and 10 variables

---