Search lines which respects request on one or more conditions.

This function looks for the lines that respect the request in either all conditions or at least one condition.

Usage

SymFilteringOperators()

qMetacellFilteringScope()

qMetacellWholeMatrix(
  object,
  cmd,
  pattern,
  percent = "Percentage",
  th,
  operator
)

qMetacellWholeLine(object, cmd, pattern)

qMetacellOnConditions(
  object,
  cmd,
  mode,
  pattern,
  conds,
  percent = "Percentage",
  operator,
  th
)

Arguments

object

An instance of the class SummarizedExperiment

cmd

A character(1) indicating the action to perform. Either "keep" or "delete".

pattern

A character() indicating the tag pattern of interest.

percent

A character(1) indicating whether the threshold represent an absolute value ("Count") or a percentage ("Percentage").

th

The threshold to apply

operator

String for operator to use. List of operators is available with 'SymFilteringOperators()'.

mode

A character(1) indicating how the task is performed. Either "AllCond" or "AtLeastOneCond".

conds

A vector of conditions in the dataset.

Value

A vector of operators

NA

A vector of filtering scopes

NA

NA

NA

Examples

SymFilteringOperators()
#>    lessthan        less greaterthan     greater       equal   different 
#>        "<="         "<"        ">="         ">"        "=="        "!=" 

data(subR25prot)
obj <- subR25prot[[1]]
level <- typeDataset(obj)
pattern <- "Missing"
mask <- match.metacell(
    metadata = qMetacell(obj),
    pattern = pattern,
    level = level
)
percent <- FALSE
th <- 3
op <- ">="
cmd <- 'delete' 
ind <- qMetacellWholeMatrix(obj, cmd, pattern, percent, th, op)

data(subR25prot)
ind <- qMetacellWholeLine(obj, cmd, pattern)

conds <- design.qf(subR25prot)$Condition
op <- ">="
th <- 0.5
percent <- "Percentage"
mode <- "AllCond"
ind <- qMetacellOnConditions(obj, cmd, mode, pattern, conds, percent, op, th)

qMetacellFilteringScope()
#> [1] "None"           "WholeLine"      "WholeMatrix"    "AllCond"       
#> [5] "AtLeastOneCond"

data(subR25prot)
obj <- subR25prot[[1]]