ozymandias-utils: for tidying up rowRanges prior to merging

In RamsinghLab/ozymandias: Tools for region- and process-centric analyses of multiple assay types

Description

for tidying up rowRanges prior to merging

mask (set to NA) beta values by pval for a GenomicRatioSet

convenience function to feed getSurv, OSurv, EFSurv

convenience function to feed OSurv, EFSurv

Get overall survival for a SummarizedExperiment-like dataset

Get event-free survival from SummarizedExperiment-like data

Usage

stripMcols(x)

maskBetas(grSet, pcutoff = 0.01, ...)

hasSurv(x, time = "time", event = "event")

getSurv(x, time = "time", event = "event")

OSurv(x, time = "OS", event = "OSevent")

EFSurv(x, time = "EFS", event = "EFSevent")

Arguments

x	a GRanges or GRangesList that has metadata columns it doesn't need
grSet	a GenomicRatioSet with matrices "Beta" and "pval"
pcutoff	optional p-value cutoff for masking, default is 0.01
time	column name for time to event covariate, default "time"
event	column name for censoring/event covariate, default "event"
x	a SummarizedExperiment-like dataset
x	a SummarizedExperiment-like dataset
time	column name for time to event, default "OS"
event	column name for censoring/event (0/1), default "OSevent"
x	a SummarizedExperiment-like dataset
time	column name for time to event, default "OS"
event	column name for censoring/event (0/1), default "OSevent"
x	a SummarizedExperiment-like dataset
time	column name for time to event, default "EFS"
event	column name for censoring/event (0/1), default "EFSevent"

Value

a boolean vector: whether each column has both covariates

a Surv object, if one can be constructed from x

a Surv object, if one can be constructed from x

a Surv object, if one can be constructed from x

Functions

• stripMcols:

• maskBetas:

• hasSurv:

• getSurv:

• OSurv:

• EFSurv:

RamsinghLab/ozymandias documentation built on May 9, 2019, 9:21 a.m.