DCARSacrossNetwork

performs DCARS method across all edges listed in the network for the (already ranked) genes x samples matrix dat

DCARSacrossNetwork(dat, edgelist, edgeNames = rownames(edgelist), ...)

Arguments

dat	a genes x samples gene expression rank matrix, should be already converted to ranks with first column lowest survival and last column highest survival
edgelist	is a 2 column character matrix with the genes to test for DCARS. if edgelist has more than 2 columns then the first two are taken
edgeNames	is the name to assign to each edge, defaults to rownames(edgelist). if edgelist has no rownames then defaults to two gene names pasted with "_" in alphabetical order
...	additional parameters passed to DCARS()

Value

value of this function depends on arguments passed into the DCARS() function (e.g. if extractTestStatisticOnly is set as TRUE)

Examples

data(STRING)
data(SKCM)
SKCM_rank = t(apply(SKCM,1,rank))

# highly significantly DCARS gene pair: SKP1 and SKP2
# calculates p-value based on permutation
DCARS(SKCM_rank,"SKP1","SKP2",plot=TRUE)
#> weight matrix not specified, generating weight matrix now
#> span not specified, defaulting to 0.5
#> performing permutation test
#> [1] 0
# extract only the test statistic
DCARS(SKCM_rank,"SKP1","SKP2", extractTestStatisticOnly = TRUE)
#> weight matrix not specified, generating weight matrix now
#> span not specified, defaulting to 0.5
#> [1] 0.227379

# not significantly DCARS gene pair: EIF3C and EIF5B
# calculates p-value based on permutation
DCARS(SKCM_rank,"EIF3C","EIF5B",plot=TRUE)
#> weight matrix not specified, generating weight matrix now
#> span not specified, defaulting to 0.5
#> performing permutation test
#> [1] 0.96
# extract only the test statistic
DCARS(SKCM_rank,"EIF3C","EIF5B", extractTestStatisticOnly = TRUE)
#> weight matrix not specified, generating weight matrix now
#> span not specified, defaulting to 0.5
#> [1] 0.01790925

# build weight matrix
W = weightMatrix(ncol(SKCM_rank), type = "triangular", span = 0.5, plot = TRUE)

# extract DCARS test statistics
SKCM_stats = DCARSacrossNetwork(SKCM_rank,edgelist = STRING,
                                W = W, extractTestStatisticOnly = TRUE,
                                verbose = FALSE)
sort(SKCM_stats,decreasing=TRUE)[1:10]
#>    GMPS_IMPDH1      SKP1_SKP2     COPB2_COPE ANAPC10_ANAPC5     TBL3_UTP18 
#>      0.2518867      0.2273790      0.2075771      0.1800155      0.1672255 
#>   PSMD12_PSMD3  POLR3B_POLR3D    RAD18_UBE2B    SNRPB_SNRPG   RPL26L1_RPL8 
#>      0.1659466      0.1629938      0.1621321      0.1555048      0.1531930