dbGetAnnotationGroupsFiltered: Get Group Annotation information from the table:...

In BenBruyneel/proteinDiscover: ProteinDiscover

Get Group Annotation information from the table: AnnotationProteinGroups. This can be done via the GroupAnnotationAccession or via the description of an annotation. When using the Description it's possible to use the SQL 'like'

Description

Get Group Annotation information from the table: AnnotationProteinGroups. This can be done via the GroupAnnotationAccession or via the description of an annotation. When using the Description it's possible to use the SQL 'like'

Usage

dbGetAnnotationGroupsFiltered(
  db,
  columns = NA,
  groupAnnotationAccession = NA,
  description = NA,
  UpperCase = FALSE,
  LowerCase = FALSE,
  like = FALSE,
  likePre = "%",
  likePost = "%",
  SQL = FALSE
)

Arguments

db	database access 'handle'
columns	allows the selection of columns to take from the table, default = NA (all columns)
groupAnnotationAccession	identification of the annotation, usually something like GO:.... (gene ontology) or pF.... (protein family). Note that when this argument is not NAm the arguments dealing with description etc are ignored
description	character vector specifying a word or sequence of word which is to be selected. If the 'like' argument is TRUE then it doesn't need to be exactly the same as the GroupAnnotationDescription field/column (in most cases the 'like' argument should be set to TRUE !)
UpperCase	if set to TRUE then BOTH description and the GroupAnnotationDescription field/column are entirely put to uppercase in the SQL used for the query. Note that if both UpperCase and LowerCase are TRUE, then UpperCase is used
LowerCase	if set to TRUE then BOTH description and the GroupAnnotationDescription field/column are entirely put to lowercase in the SQL used for the query.
like	if set to TRUE then the SQL 'LIKE' in stead of 'IN' is used to query the data. This only applies when the argument 'discription' is used. This is ignored when 'GroupAnnotationAccession' is used. If like = TRUE, then using eg 'locomotion' will result in the SQL query being: WHERE ... LIKE ' resulting table will give all rows, where the description part contains 'locomotion'. If like = FALSE, then only rows where the description exactly matches 'locomotion' will be selected. It's also possible to use the '_' (underscore) to make the LIKE function more or less specific. See eg SQL LIKE Operator for more info
likePre	default is ' 'description' argument to facilitate (partial) matching. It's better to set to ” (empty string) when creating LIKE arguments directly via the 'description' argument
likePost	default is ' of the 'description' argument to facilitate (partial) matching. It's better to set to ” (empty string) when creating LIKE arguments directly via the 'description' argument
SQL	allows the function to return the SQL query statement in stead of a data.frame

Value

a data.frame or a character vector (SQL)

BenBruyneel/proteinDiscover documentation built on March 16, 2024, 4:36 p.m.