aggregateRanks: Aggreagate ranks from multiple sources with various methods

In miRNAtap: miRNAtap: microRNA Targets - Aggregated Predictions

Description

This function performs aggregation phase of target prediction for getPredictedTargets. Consensus ranking is derived from multiple individual rankings. Available methods include minimum, maximum and geometric mean with further tuning parameters which promote true positives at the top of the final ranking

Usage

aggregateRanks(ranks, n_valid_srcs, min_src, method = "geom",
  promote = TRUE)

Arguments

ranks	data.frame with ordered scores
n_valid_srcs	number of valid sources in the dataset
min_src	minimum acceptable number fo sources
method	'min','max', or 'geom', default 'geom'
promote	add weights to improve accuracy of the method, default TRUE

Value

data.frame object with ranks per source and aggregate ranks

Author(s)

Maciej Pajak [e-mail]

Examples

data = data.frame(GeneID=c("15364", "56520", "57781", "58180", "18035"),
                source1scores=c(0.9,0.5,0.3,NA,NA),
                source2scores=c(0.7,NA,0.8,0.6,0.5),
                source3scores=c(0.5,NA,0.3,0.1,0.2))
data #dataframe with scores
aggregateRanks(data, n_valid_srcs=3, min_src=2, method='geom')
#note how gene 56520 is eliminated as it appeared in fewer than 2 sources

Example output

Loading required package: AnnotationDbi
Loading required package: stats4
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

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

  GeneID source1scores source2scores source3scores
1  15364           0.9           0.7           0.5
2  56520           0.5            NA            NA
3  57781           0.3           0.8           0.3
4  58180            NA           0.6           0.1
5  18035            NA           0.5           0.2
      source_1 source_2 source_3 rank_product rank_final
15364        1        2        1    0.4199737        1.0
57781        2        1        2    0.5291337        2.0
58180       NA        3        4    1.7320508        3.5
18035       NA        4        3    1.7320508        3.5

miRNAtap documentation built on Nov. 8, 2020, 8:12 p.m.