separate_flag: separate plate flags into well flags
In olobiolo/siscreenr: Analyze Genome-Wide siRNA Screening Campaigns

Description Usage Arguments Details Value Well identifiers Caution See Also

If a column in a screen object contains a string with a list of wells of interest, convert it into a logical vector that flags individual wells.

separate_flag(
  scr,
  flag = "wells_rescanned",
  newname,
  sep = ", ",
  well.ID = "position"
)

`scr`	a screen object, i.e. a `data.frame`
`flag`	name of column to transform, given as character
`newname`	optional new name for the `flag` column, given as string
`sep`	splitting terms for `flag` strings, passed to `strsplit`
`well.ID`	name of column with well identifier, given as character; see `Well identifiers`

During the screening campaign hardware or software errors may occur that could potentially affect individual wells or whole plates. This should be kept in mind and will typically be noted in the screen log file. If a problem is persistent, it is prudent to create a dedicated column to keep track of affected wells.

Since the screen log is based on plates and flags may concern individual wells, all problematic wells in a plate will likely be enumerated such that upon reading the log file, they will be contained in a single string, e.g. "A1, H17".

In order to improve legibility of the screen report these comments, rather than be repeated as is for all wells, they will be converted into a logical flag, where the noted wells will get a TRUE value and the others will get a FALSE.

Comments that read "all" or "whole plate" will flag all wells in that plate.

a data frame where the flag variable was converted from string to logical and optionally renamed

A well can be identified in two ways: by a number from 1 through the number of wells in a plate or by its row/column coordinates, e.g. "A3". ScanR automatically assigns the former into a column called "Index". This is renamed to "well" by build_screen. ScanR also puts the latter into a column called "Description" but I recommend to disregard it as it may cause problems if the export file is defined by groups rather than wells. Well coordinates can be introduced by the layout file, typically in a single column called "position" or in two columns called "row" and "column", or both.

It is crucial that notes in a flagging column are kept consistent, i.e. use either the well number or position. Also, when using position, pay attention to whether you use a strict 3-character format or a loose one, that is whether you call an "A2" well "A2" or "A02". Keep this consistent between your files.

insert_zeros

olobiolo/siscreenr documentation built on Nov. 26, 2021, 3:08 p.m.