resolveMaps {AnnBuilder}R Documentation

Functions to obtain unified mappings for a given set of ids using various sources

Description

These functions are used to obtain unified mappings between two sets of ids based on the mappings available from different sources. Each source provide mappings between two sets of ids.

Usage

resolveMaps(maps, trusted, srcs, colNames = NULL, outName = "", asFile = TRUE)
getVote(voters, sep = ";")
getUnified(voters)
getNoDup(voters)
hasDelimit(entry, deli = ";") 

Arguments

maps maps a matrix with mappings for a set of key ids to another set of ids provided by different sources. The first column is assumed to be the key ids and the rest are mappings to another set of ids provided by different sources
trusted trusted a vector of characters to indicate the column number of "maps" whose mappings are more reliable and should be used when there are conflicts among sources
srcs srcs a vector of character strings for the names of columns that contain mappings from different sources
colNames colNames a vector of character strings for the names of columns in "maps"
outName outName a character string for the name of the file to contain the unified mappings
asFile asFile a boolean to indicate whether the unified mappings will be saved as a file
voters voters a vector containing mappings from different sources
entry entry a character string to be checked for the existence of a separator
deli deli a character string for a separator
sep sep same as deli

Details

Each source may have different mappings from the key ids to another set of ids. resolveMaps resolves the conflicts and derives a set of unified mappings based on the mappings provided from several sources.

getVote resolves the mappings for a given key id and returns a vector with unified mapping and the number of sources that agree with the unified mapping.

getUnified finds agreement among values in a vector passed. If some values agree, get the one agreed by most sources.

getNoDup gets a value based on predefined rules when values from different sources do not agree.

hasDelimit checks to see if a delimiter exists

Value

resolveMaps returns a matrix with the first column being the key id set, second being the unified mappings to another id set, and third the total number of agreements found among sources.
getVote returns a two element vector.
getUnified returns a character string.
getNoDup returns a character string.
hasDelimit returns TRUE or FALSE.

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

See Also

LL-class, UG-class

Examples

maps <- matrix(c("id1", "a", "a", "b", "id2", "c","d", "c",
"id3", "e","e", "e", "id4", NA, "f", NA, "id5", "g", NA, "h", "id6", NA,
"NA", "i", "id7", NA, NA, NA), ncol = 4, byrow = TRUE)
unified <- resolveMaps(maps, c("srcll", "srcug"),
c("srcll", "srcug", "srcgeo"),
colNames = c("key1", "srcll", "srcug", "srcgeo"), outName = "",
asFile = FALSE)

[Package AnnBuilder version 1.4.21 Index]