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SJD Wrap

Source: R/sjdWrap.R
sjdWrap.Rd

wrapping up expression matrices (of different species) with only shared genes as SJD input

Usage

sjdWrap(
  data.list,
  species.vector,
  geneType.vector,
  geneType.out = "symbol",
  species.out
)

Arguments

data.list

input list of expression matrices from different species i.e human and mouse datasets

species.vector

character of species type of each matrix i.e c('human', 'mouse', 'mouse')

geneType.vector

character of gene/rowname type of each matrix i.e c("symbol","ensembl","symbol")

geneType.out

character of output gene/rowname type of each matrix i.e "symbol"

species.out

character of output species type for gene/rowname

Value

A list of expression matrices (of different species) with only shared genes

Examples


data(NeuroGenesis4)
SJDdataIN = sjdWrap(
data.list = NeuroGenesis4,
species.vector=c("human","human","human","mouse"),
geneType.vector=c("symbol","ensembl","symbol","symbol"),
geneType.out="symbol",
species.out="human")
#> Using biomaRt to connect gene IDs across 4 datasets:
#> Getting biomaRt IDs for dataset 1 
#> You have input  40  genes
#> We found  40  matches
#> 1  of those are duplicates and only keeping the 1st of each
#> Getting biomaRt IDs for dataset 2 
#> You have input  40  genes
#> We found  37  matches
#> 1  of those are duplicates and only keeping the 1st of each
#> Getting biomaRt IDs for dataset 3 
#> You have input  40  genes
#> We found  39  matches
#> 0  of those are duplicates and only keeping the 1st of each
#> Getting biomaRt IDs for dataset 4 
#> You have input  40  genes
#> We found  31  matches
#> 0  of those are duplicates and only keeping the 1st of each
#> constructed 4 tables of cross-species matching genes
#> we found 24 shared genes in 4 datasets
#> new data list of 4 datasets constructed