getColumn: getColumn

In CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

Description

Use simple pattern matching to try to identify a column in a data.frame or equivalent by its name

Usage

getColumn(df, col=NULL, pattern="", avoid.pattern = NULL, msg.col.name="", needed=TRUE, verbose = TRUE)

Arguments

df	(data.frame or equivalent) The object were columns are searched. It must be either a data.frame or an object where names(df) works.
col	(number or character) The column to identify. If NULL an heuristic will be used to automatically identify the column. It can also a number or a character to define the exact column to return.(defaults to NULL)
pattern	(character) The pattern to match the column name. If more than one column matches the pattern, the first one (leftmost) will be returned. The pattern may be any valid regular expression. (defaults to "")
avoid.pattern	(character) The pattern to avoid on the column name. The pattern may be any valid regular expression. (defaults to "")
msg.col.name	(character) Only used in the error message to make the message clearer. The name of the column we are searching for. (defaults to "")
needed	(logical) Whether the column is needed or not. If TRUE, an error will be raised if the column is not found. (defaults to TRUE)
verbose	(logical) Whether to show information messages. (defaults to TRUE)

Details

This function will use pattern matching to try to identify which column of a data.frame contains a certain data. It will return its number. If col is specified it will not use pattern matching but identify if a column with that exact name exists and return its position.

Value

The number of the column matching the specification or NULL if no column was found.

Examples

df <- data.frame("id"= "rs1234", "endogenous" = FALSE, "chromosome"="chr1", "Start"=0, "end.position"=100,
"copy.number.level"=3, "LOH"=0, "median.value.per.segment"=1.2,
"BAF"=0.2, "Log Ratio"=1.5,  "strange.name"="strange.value")

col.num <- getColumn(df = df, pattern = "Chr|chr",  msg.col.name = "Chromosome", needed = TRUE)
col.num <- getColumn(df = df, col = "chromosome",  msg.col.name = "Chromosome", needed = TRUE)
col.num <- getColumn(df = df, col = 3, msg.col.name = "Chromosome", needed = TRUE)


col.num <- getColumn(df = df, pattern = "end",  msg.col.name = "End", needed = TRUE)
col.num <- getColumn(df = df, pattern = "end", avoid.pattern = "endogenous", msg.col.name = "End", needed = TRUE)

CopyNumberPlots documentation built on Nov. 8, 2020, 6:51 p.m.