- Home
- CRAN
**MAMA**: Meta-Analysis of MicroArray**gene.list**: Intersect of gene lists

# Intersect of gene lists

### Description

This function takes list of gene list as input and returns a matrix of gene names common in pairs of lists

### Usage

1 | ```
gene.list(lists)
``` |

### Arguments

`lists` |
list of vectors. Each vector refers to a method and contains names of significant genes |

### Details

Simmilar to `conting.tab`

and `Z`

, but provides different output

### Value

A matrix of gene names common in two gene lists

### Author(s)

Ivana Ihnatova

### See Also

`conting.tab`

, `Z`

### Examples

1 2 3 4 |

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker. Vote for new features on Trello.

- clinical: Functions to retrieve and assign
- clinical: Functions to retrieve and assign
- clinical.sum: Function to calculate summaries of clinical data
- clinical.sum: Function to calculate summaries of clinical data
- colIntersect: Function to find intersect in columns of a data.frame
- colIntersect: Function to find intersect in columns of a data.frame
- ColonData: Example dataset for meta-analysis of microarray
- ColonData: Example dataset for meta-analysis of microarray
- commonGenes: Function to compute number of common genes in ordered gene...
- commonGenes: Function to compute number of common genes in ordered gene...
- computeAlpha: Function to do compute tunning parameter alpha
- computeAlpha: Function to do compute tunning parameter alpha
- computeOrdering: Function to compute ordered gene lists
- computeOrdering: Function to compute ordered gene lists
- compute.RQ: Function to compute R and Q statistics as defined in - see...
- compute.RQ: Function to compute R and Q statistics as defined in - see...
- conting.tab: Contingency table from gene lists
- conting.tab: Contingency table from gene lists
- cv.filter: Microarray probes filtering
- cv.filter: Microarray probes filtering
- entitybuild2: Function to calculate test statistic for microarray data
- entitybuild2: Function to calculate test statistic for microarray data
- ES.GeneMeta: Wrapper function for combining the effect size as implemented...
- ES.GeneMeta: Wrapper function for combining the effect size as implemented...
- flip: Function to flip data frames
- flip: Function to flip data frames
- fold.change: Function to do compute fold change between two groups
- fold.change: Function to do compute fold change between two groups
- gene.list: Intersect of gene lists
- gene.list: Intersect of gene lists
- gene.select.FC: Function to select genes according to fold change
- gene.select.FC: Function to select genes according to fold change
- join.DEG: Function to join vectors of differentially expressed genes to...
- join.DEG: Function to join vectors of differentially expressed genes to...
- join.results: Function to join results from meta-analysis to one list
- join.results: Function to join results from meta-analysis to one list
- make.matrix: Function to make matrix for heatmap to compare results of...
- make.matrix: Function to make matrix for heatmap to compare results of...
- MAP.genes: Function to do assign probesets IDs to patterns
- MAP.genes: Function to do assign probesets IDs to patterns
- MAP.Matches: Wrapper function for MAP-Matches method
- MAP.Matches: Wrapper function for MAP-Matches method
- MAPmatrix: Function to summarize binary matrix
- MAPmatrix: Function to summarize binary matrix
- MAPsig1: Pattern signifficance
- MAPsig1: Pattern signifficance
- MAPsig2: Pattern signifficance
- MAPsig2: Pattern signifficance
- MCtest: Monte Carlo permutation test
- MCtest: Monte Carlo permutation test
- mergedata: Function to merge data from MetaArray object
- mergedata: Function to merge data from MetaArray object
- MetaArray: Class "MetaArray" ~~~
- MetaArray: Class "MetaArray" ~~~
- metagene: Function to do extract row from list of data.frames
- metaheat: Display Data as Heatmap
- metaheat: Display Data as Heatmap
- metaheat2: Function to plot heatmap
- metaheat2: Function to plot heatmap
- metalist.to.matrix: Function to do convert list to matrix
- metalist.to.matrix: Function to do convert list to matrix
- metaMA: Wrapper function for effect size or p-value combination...
- metaMA: Wrapper function for effect size or p-value combination...
- meta.test: Function to compute T-statistic and p-value in meta-analysis
- meta.test: Function to compute T-statistic and p-value in meta-analysis
- methods: Replacement Methods for 'MetaArray' object
- methods: Replacement Methods for 'MetaArray' object
- METRADISC: Wrapper function for METRADISC method
- METRADISC: Wrapper function for METRADISC method
- patternMatch: Function to count soft pattern matches
- patternMatch: Function to count soft pattern matches
- patternMatch.strong: Function to count strong pattern matches
- patternMatch.strong: Function to count strong pattern matches
- patternmatrix: Function to split binary vectors to matrix.
- patternmatrix: Function to split binary vectors to matrix.
- patternToString: Function to convert rows of a matrix to strings
- patternToString: Function to convert rows of a matrix to strings
- performSOGL: Function to perform analysis using Similarity of Ordered Gene...
- performSOGL: Function to perform analysis using Similarity of Ordered Gene...
- plotES: Function to do plots in combination of effect size method
- plotES: Function to do plots in combination of effect size method
- plotgene: Function to visuaze change in expression of one gene
- plotgene: Function to visuaze change in expression of one gene
- plotgene2: Function to visuaze change in expression of one gene
- plotgene2: Function to visuaze change in expression of one gene
- plotpattern: Function to do plot signifficance of Meta-Analysis Patterns
- plotpattern: Function to do plot signifficance of Meta-Analysis Patterns
- plotQvsChi: Function to plot quantiles of Cochran's Q statistic and...
- plot.SOGLresult: Function to plot an object of class SOGLresult
- plot.SOGLresult: Function to plot an object of class SOGLresult
- prelimScore: Function compute preliminary Similarity Score for Ordered...
- prelimScore: Function compute preliminary Similarity Score for Ordered...
- prepareData: Function to prepare data
- prepareData: Function to prepare data
- preparePermutations: Function to prepare permutation and subsamples
- preparePermutations: Function to prepare permutation and subsamples
- probs.to.matrix: Function to convert list to matrix
- probs.to.matrix: Function to convert list to matrix
- RandomScore: Function to do compute random and subsampled similarity score
- RandomScore: Function to do compute random and subsampled similarity score
- rank.genes: Rank genes
- rank.genes: Rank genes
- rank.genes.adv: Function to rank genes
- rank.genes.adv: Function to rank genes
- RankProduct: Wrapper function for RankProduct method
- RankProduct: Wrapper function for RankProduct method
- ratio: Function to calculate the ratio of co-significant:...
- ratio: Function to calculate the ratio of co-significant:...
- sd.filter: Microarray probes filtering
- sd.filter: Microarray probes filtering
- selectAlpha: Function to select the most optimal alpha parameter
- selectAlpha: Function to select the most optimal alpha parameter
- selectClass: Function to select class labels from MetaArray object
- selectClass: Function to select class labels from MetaArray object
- selectGenes: Function to select genes that account for Similarity score
- selectGenes: Function to select genes that account for Similarity score
- sigScore: Function to calculate signifficance of similarity score
- sigScore: Function to calculate signifficance of similarity score
- test.group.shuffle: Function to do compute test statistic iterativelly
- test.group.shuffle: Function to do compute test statistic iterativelly
- T.select: Function to help with selection of threshold for T-statistics
- T.select: Function to help with selection of threshold for T-statistics
- VennMapper: Wrapper function for VennMapping
- VennMapper: Wrapper function for VennMapping
- Z: Function to compute Z-statistics in contingency table
- Z: Function to compute Z-statistics in contingency table
- zScores: Function for Meta-analysis of gene expression data
- zScores: Function for Meta-analysis of gene expression data