resolveMaps {AnnBuilder} | R Documentation |
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.
resolveMaps(maps, trusted, srcs, colNames = NULL, outName = "", asFile = TRUE) getVote(voters, sep = ";") getUnified(voters) getNoDup(voters) hasDelimit(entry, deli = ";")
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 |
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
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.
The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua Zhang
## Not run: 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) ## End(Not run)