tpcaResult-class: S4 TPCA Result Class

In Rtpca: Thermal proximity co-aggregation with R

Description

S4 TPCA Result Class

Value

an object of class tpcaResult with the following slots: 1) ObjList: containing the supplied list of objects (e.g. a list of Expression Sets summarizing a TPP experiment) 2) ContrastList: containing the supplied list of constrast objects (if supplied for performance of a differential Rtpca analysis) 3) CtrlCondName: character string indicating the control condition, e.g. "control" 4) ContrastCondName: character string indicating the contrast condition, e.g. "drug treatment" 5) DistMat: a matrix containing all pairwise protein-protein distances obtained from comparing their melting curves in the control condition 6) ContrastDistMat: a matrix containing all pairwise protein-protein distances obtained from comparing their melting curves in the contrast condition 7) CommonFeatures: a vector containing the features (proteins) found in common between control and contrast condition 8) ComplexAnnotation: a data frame supplied by the user annotating protein to protein complexes 9) ComplexBackgroundDistributionList: a list of distances drawn for random groups of proteins with different number of members 10) PPiAnnotation: a data frame supplied by the user annotating protein-protein interactions 11) PPiRocTable: data frame containing false positive rate and true positive rate based on ranking the TPCA analysis results by euclidean distance of melting curves of protein pairs, annotated PPIs are considered true positives 12) PPiRocTableAnno: annotation to PPiRocTable 13) ComplexRocTable: data frame containing false positive rate and true positive rate based on ranking the TPCA analysis results by euclidean distance of melting curves of proteins within annotated complexes, annotated complexes are considered true positives, proteins in randomly permuted complex annotations are considered false positives 14) summaryMethod: character string of summarization method used to summarize data across replicates 15) distMethod: character string of distance method used to compare melting curves of proteins 16) tpcaResultTable: data frame containing the results from a tpca analysis 17) diffTpcaResultTable: data frame containing the results from a differential tpca analysis

Slots

ObjList

list.

ContrastList

list.

CtrlCondName

character.

ContrastCondName

character.

DistMat

matrix.

ContrastDistMat

matrix

CommonFeatures

vector.

ComplexAnnotation

data.frame.

ComplexBackgroundDistributionList

list.

PPiAnnotation

data.frame.

PPiRocTable

data.frame

PPiRocTableAnno

data.frame

ComplexRocTable

data.frame

summaryMethod

character.

distMethod

character.

tpcaResultTable

data.frame.

diffTpcaResultTable

data.frame.

Examples

m1 <- matrix(1:12, ncol = 4)
m2 <- matrix(2:13, ncol = 4)
m3 <- matrix(c(2:10, 1:7), ncol = 4)

rownames(m1) <- 1:3
rownames(m2) <- 2:4
rownames(m3) <- 2:5

mat_list <- list(
    m1, m2, m3
)
tpcaObj <- new("tpcaResult", ObjList = mat_list)

Rtpca documentation built on Nov. 8, 2020, 7:44 p.m.