allHR: For all possible separation points for a cohort ordered by a...
In survivALL: Continuous Biomarker Assessment by Exhaustive Survival Analysis
Description
Usage
Arguments
Value
Examples
Description
For all possible separation points for a cohort ordered by a continuous
measurement, calculate hazard ratio
Usage
1
2
Arguments
measure
A continuous variable used to order survival data. Samples
must be ordered exactly as in srv
srv
A dataframe that contains at least two columns, detailing event
and time to event information.
Samples must be ordered exactly as in measure
time
Column name in srv containing time to event information. Must
not contain NAs
event
Column name in srv containing event information coded as 0 (no
event) and 1 (event). Must not contain NAs
log2HR
Hazard ratios are returned as log2 values by default
remove_outliers
Large hazard ratios result from statistical
disproportion when considering edge cases (e.g. 1 vs 99) and can be
automaticall removed
Value
A vector of hazard ratios calculated from srv ordered by
measure
Examples
1
2
3
4
5
6
library(survivALL)
data(nki_subset)
library(Biobase)
gene_vec <- exprs(nki_subset)["NM_004448", ] #ERBB2 gene id
allHR(measure = gene_vec, srv = pData(nki_subset), time = "t.dmfs",
event = "e.dmfs", log2HR = TRUE)
Example output
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: survival
[1] -4.563397e+00 -8.904506e-01 1.816569e-01 -4.029330e-01 -8.401771e-01
[6] -1.191478e+00 -1.402118e+00 -1.055405e+00 -9.255842e-01 -9.255842e-01
[11] -1.175258e+00 -8.873963e-01 -6.852524e-01 -5.391589e-01 -4.131288e-01
[16] -2.512127e-01 -1.206927e-01 -2.146303e-02 -2.050834e-01 -4.058750e-01
[21] -3.155729e-01 -4.371582e-01 -5.364837e-01 -4.376606e-01 -5.600368e-01
[26] -6.369136e-01 -5.739293e-01 -6.651362e-01 -5.837484e-01 -5.211401e-01
[31] -6.271721e-01 -5.729967e-01 -6.632566e-01 -6.097701e-01 -5.602157e-01
[36] -4.892275e-01 -5.960711e-01 -5.483365e-01 -6.351773e-01 -5.840102e-01
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[81] -6.040544e-01 -5.653556e-01 -5.251042e-01 -5.029171e-01 -4.802447e-01
[86] -4.567379e-01 -4.226622e-01 -4.720089e-01 -4.409661e-01 -4.153124e-01
[91] -3.745726e-01 -3.466121e-01 -3.120517e-01 -3.000890e-01 -3.553261e-01
[96] -3.968110e-01 -4.278768e-01 -4.027209e-01 -4.314542e-01 -4.767928e-01
[101] -4.554647e-01 -4.319147e-01 -3.974804e-01 -3.733358e-01 -3.450940e-01
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[116] -2.685917e-01 -2.385699e-01 -2.191872e-01 -1.878238e-01 -1.689194e-01
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[156] -5.030739e-02 -2.548464e-02 2.069530e-05 3.129450e-02 5.869993e-02
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[206] -1.271373e-02 2.218190e-02 -2.059843e-02 -2.247647e-04 2.789049e-02
[211] 4.815416e-02 5.147015e-03 5.147015e-03 2.500150e-02 4.878753e-02
[216] 6.946798e-02 2.404177e-02 6.085910e-02 9.807781e-02 1.297213e-01
[221] 1.606414e-01 1.820043e-01 2.084305e-01 2.320082e-01 2.541691e-01
[226] 2.785115e-01 3.070268e-01 3.388151e-01 3.653849e-01 3.881715e-01
[231] 4.243007e-01 4.483051e-01 4.149335e-01 4.542602e-01 4.635339e-01
[236] 4.880030e-01 5.179544e-01 5.457324e-01 5.714134e-01 5.903955e-01
[241] 6.165443e-01 5.934508e-01 6.198433e-01 5.637545e-01 6.109976e-01
[246] 6.594140e-01 7.091542e-01 6.493001e-01 6.854417e-01 7.142922e-01
[251] 6.754753e-01 6.216578e-01 6.646872e-01 6.128616e-01 6.469178e-01
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[266] 7.707343e-01 7.303315e-01 6.868476e-01 7.321857e-01 7.712937e-01
[271] 8.259354e-01 8.708353e-01 9.402412e-01 1.005742e+00 1.006143e+00
[276] 9.699776e-01 1.053669e+00 1.104927e+00 1.026267e+00 1.095541e+00
[281] 1.024513e+00 1.051300e+00 1.116784e+00 1.200944e+00 1.109240e+00
[286] 1.166856e+00 1.069346e+00 1.135827e+00 1.047378e+00 1.111144e+00
[291] 1.202654e+00 1.126347e+00 1.029671e+00 9.534647e-01 1.036446e+00
[296] 1.110168e+00 1.201982e+00 1.090189e+00 1.218301e+00 1.171843e+00
[301] 1.320401e+00 1.168608e+00 1.371442e+00 1.288083e+00 1.228491e+00
[306] 1.378997e+00 1.184556e+00 1.370015e+00 1.177955e+00 1.039435e+00
[311] 1.368074e+00 1.217621e+00 8.957515e-01 3.559031e-01 1.044744e+00
[316] NA 1.843580e+00 -2.020620e+01 NA
survivALL documentation built on May 1, 2019, 11:02 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Examples
Description
For all possible separation points for a cohort ordered by a continuous measurement, calculate hazard ratio
Usage
1 2 |
Arguments
measure |
A continuous variable used to order survival data. Samples must be ordered exactly as in srv |
srv |
A dataframe that contains at least two columns, detailing event and time to event information. Samples must be ordered exactly as in measure |
time |
Column name in srv containing time to event information. Must not contain NAs |
event |
Column name in srv containing event information coded as 0 (no event) and 1 (event). Must not contain NAs |
log2HR |
Hazard ratios are returned as log2 values by default |
remove_outliers |
Large hazard ratios result from statistical disproportion when considering edge cases (e.g. 1 vs 99) and can be automaticall removed |
Value
A vector of hazard ratios calculated from srv ordered by
measure
Examples
1 2 3 4 5 6 | library(survivALL)
data(nki_subset)
library(Biobase)
gene_vec <- exprs(nki_subset)["NM_004448", ] #ERBB2 gene id
allHR(measure = gene_vec, srv = pData(nki_subset), time = "t.dmfs",
event = "e.dmfs", log2HR = TRUE)
|
Example output
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: survival
[1] -4.563397e+00 -8.904506e-01 1.816569e-01 -4.029330e-01 -8.401771e-01
[6] -1.191478e+00 -1.402118e+00 -1.055405e+00 -9.255842e-01 -9.255842e-01
[11] -1.175258e+00 -8.873963e-01 -6.852524e-01 -5.391589e-01 -4.131288e-01
[16] -2.512127e-01 -1.206927e-01 -2.146303e-02 -2.050834e-01 -4.058750e-01
[21] -3.155729e-01 -4.371582e-01 -5.364837e-01 -4.376606e-01 -5.600368e-01
[26] -6.369136e-01 -5.739293e-01 -6.651362e-01 -5.837484e-01 -5.211401e-01
[31] -6.271721e-01 -5.729967e-01 -6.632566e-01 -6.097701e-01 -5.602157e-01
[36] -4.892275e-01 -5.960711e-01 -5.483365e-01 -6.351773e-01 -5.840102e-01
[41] -6.776861e-01 -6.050110e-01 -5.626040e-01 -5.149043e-01 -5.923201e-01
[46] -5.407762e-01 -4.906093e-01 -5.470015e-01 -5.076781e-01 -4.677617e-01
[51] -4.245598e-01 -4.833733e-01 -5.147577e-01 -4.749661e-01 -5.316229e-01
[56] -4.820245e-01 -5.573695e-01 -6.281806e-01 -5.962104e-01 -5.673602e-01
[61] -5.308118e-01 -5.756829e-01 -5.280735e-01 -5.743993e-01 -5.583731e-01
[66] -5.100191e-01 -4.628308e-01 -5.191748e-01 -4.872644e-01 -5.339017e-01
[71] -5.013285e-01 -4.632849e-01 -4.974087e-01 -4.875841e-01 -5.456777e-01
[76] -5.050213e-01 -5.554418e-01 -5.961544e-01 -5.894165e-01 -5.528097e-01
[81] -6.040544e-01 -5.653556e-01 -5.251042e-01 -5.029171e-01 -4.802447e-01
[86] -4.567379e-01 -4.226622e-01 -4.720089e-01 -4.409661e-01 -4.153124e-01
[91] -3.745726e-01 -3.466121e-01 -3.120517e-01 -3.000890e-01 -3.553261e-01
[96] -3.968110e-01 -4.278768e-01 -4.027209e-01 -4.314542e-01 -4.767928e-01
[101] -4.554647e-01 -4.319147e-01 -3.974804e-01 -3.733358e-01 -3.450940e-01
[106] -3.115225e-01 -3.496874e-01 -3.997568e-01 -3.783815e-01 -3.578466e-01
[111] -3.279985e-01 -2.971776e-01 -2.747073e-01 -2.442685e-01 -2.976381e-01
[116] -2.685917e-01 -2.385699e-01 -2.191872e-01 -1.878238e-01 -1.689194e-01
[121] -1.689194e-01 -1.429242e-01 -1.235600e-01 -1.024884e-01 -6.918051e-02
[126] -5.066871e-02 -2.380799e-02 8.993664e-03 -4.522413e-02 -8.739076e-02
[131] -6.681554e-02 -4.861548e-02 -7.867466e-02 -6.029515e-02 -2.803672e-02
[136] -5.604167e-02 -1.027523e-01 -8.483202e-02 -5.535385e-02 -3.693624e-02
[141] -7.709971e-02 -1.268587e-01 -9.506429e-02 -6.734501e-02 -4.809526e-02
[146] -2.734289e-02 -5.155158e-02 -9.419626e-02 -7.469817e-02 -5.522131e-02
[151] -3.264169e-02 -1.507953e-02 1.131561e-02 2.912401e-02 -4.890840e-03
[156] -5.030739e-02 -2.548464e-02 2.069530e-05 3.129450e-02 5.869993e-02
[161] 7.648070e-02 1.028465e-01 1.270615e-01 9.381437e-02 5.319798e-02
[166] 5.525762e-02 7.308336e-02 9.566004e-02 7.396478e-02 2.199751e-02
[171] 5.345163e-02 2.134072e-02 3.926680e-02 4.082004e-03 -3.929865e-02
[176] -6.985492e-02 -1.180572e-01 -1.473823e-01 -1.245248e-01 -1.695681e-01
[181] -1.514388e-01 -1.332813e-01 -1.679103e-01 -1.417749e-01 -1.214700e-01
[186] -9.518855e-02 -6.531211e-02 -4.684707e-02 -8.826481e-02 -6.238538e-02
[191] -4.037290e-02 -1.962764e-02 -6.803509e-02 -4.719869e-02 -8.343780e-02
[196] -5.013847e-02 -2.768449e-02 -7.244228e-02 -1.235210e-01 -9.242169e-02
[201] -7.215457e-02 -5.312292e-02 -1.894072e-02 -7.537917e-02 -4.734725e-02
[206] -1.271373e-02 2.218190e-02 -2.059843e-02 -2.247647e-04 2.789049e-02
[211] 4.815416e-02 5.147015e-03 5.147015e-03 2.500150e-02 4.878753e-02
[216] 6.946798e-02 2.404177e-02 6.085910e-02 9.807781e-02 1.297213e-01
[221] 1.606414e-01 1.820043e-01 2.084305e-01 2.320082e-01 2.541691e-01
[226] 2.785115e-01 3.070268e-01 3.388151e-01 3.653849e-01 3.881715e-01
[231] 4.243007e-01 4.483051e-01 4.149335e-01 4.542602e-01 4.635339e-01
[236] 4.880030e-01 5.179544e-01 5.457324e-01 5.714134e-01 5.903955e-01
[241] 6.165443e-01 5.934508e-01 6.198433e-01 5.637545e-01 6.109976e-01
[246] 6.594140e-01 7.091542e-01 6.493001e-01 6.854417e-01 7.142922e-01
[251] 6.754753e-01 6.216578e-01 6.646872e-01 6.128616e-01 6.469178e-01
[256] 6.864832e-01 7.210800e-01 6.548807e-01 7.079817e-01 7.448134e-01
[261] 7.839451e-01 8.375437e-01 7.684906e-01 7.042006e-01 7.172599e-01
[266] 7.707343e-01 7.303315e-01 6.868476e-01 7.321857e-01 7.712937e-01
[271] 8.259354e-01 8.708353e-01 9.402412e-01 1.005742e+00 1.006143e+00
[276] 9.699776e-01 1.053669e+00 1.104927e+00 1.026267e+00 1.095541e+00
[281] 1.024513e+00 1.051300e+00 1.116784e+00 1.200944e+00 1.109240e+00
[286] 1.166856e+00 1.069346e+00 1.135827e+00 1.047378e+00 1.111144e+00
[291] 1.202654e+00 1.126347e+00 1.029671e+00 9.534647e-01 1.036446e+00
[296] 1.110168e+00 1.201982e+00 1.090189e+00 1.218301e+00 1.171843e+00
[301] 1.320401e+00 1.168608e+00 1.371442e+00 1.288083e+00 1.228491e+00
[306] 1.378997e+00 1.184556e+00 1.370015e+00 1.177955e+00 1.039435e+00
[311] 1.368074e+00 1.217621e+00 8.957515e-01 3.559031e-01 1.044744e+00
[316] NA 1.843580e+00 -2.020620e+01 NA
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