allow for multiple filtering in subset_targets

[tjthurman]

I think both @jbird9 and @dhalkam have run into this issue at different points. Currently, subset_targets() only filters on one column at a time (though you can filter out multiple strings for that column). So, filtering on multiple columns (e.g., filter out "Pool" samples from the group column, then filtering a specific sample from the the sample column) requires running subset_targets() twice. This is also a little un-intuitive. In the pipeline, the main input to subset_targets() is the targets dataframe made by make_targets(), but the output of subset_targets() is a list, where the first element is the targets data frame. So, to filter twice, the current code is kinda awkward:

targets <- make_targets(...)
filter1 <- subset_targets(targets, filter_column = "group", rm.vals = "Pool")
final_targets <- subset_targets(filter1$targets, filter_column = "sample", rm.vals = c("sampleA", "sampleB")

Might be nice to change this so that you can do all the filtering at once. Maybe by filtering on a named list, where the name is the column and the list element is the stuff to get filtered, e.g.:

targets <- make_targets(...)
final_targets <- subset_targets(targets, 
                                filter = list("group" = c("Pool"),
                                              "sample" = c("sampleA", "sampleB")))

[clw09]

sounds good

Cheers!

Charity L. Washam, PhD

Instructor of Biochemistry and Molecular Biology

Bioinformatician, UAMS Bioinformatics Core

University of Arkansas for Medical Sciences

4301 W Markham St., Slot 516

Little Rock, Arkansas 72205

Bioinformatician, CTPR Genomics and Bioinformatics Resource

Center for Translational Pediatric Research (CTPR)

(www.archildrens.org/archildrens-COBRE)

Arkansas Children's Research Institute (ACRI)

13 Children’s Way, Slot 512-47

Little Rock, Arkansas 72202-3591

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From: Tim Thurman @.> Sent: Wednesday, May 11, 2022 10:07:29 AM To: ByrumLab/proteomicsDIA @.> Cc: Subscribed @.***> Subject: [ByrumLab/proteomicsDIA] allow for multiple filtering in subset_targets (Issue #25)

I think both @jbird9https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jbird9&d=DwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=E045ukXXqOEQLWSfZLobKA&m=Z2yee8UgQDB2wvyRaak-cX38FsJP0PhBwpRR8druzr8&s=AX1GvnO3-Vz-iTvgwbNjm6mfFbX9dE8KkZepH7y8KLI&e= and @dhalkamhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dhalkam&d=DwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=E045ukXXqOEQLWSfZLobKA&m=Z2yee8UgQDB2wvyRaak-cX38FsJP0PhBwpRR8druzr8&s=P5nd2ZtYeKFKqv4clnaT2VVjRgvMHirUkxlOWqRv6-I&e= have run into this issue at different points. Currently, subset_targets() only filters on one column at a time (though you can filter out multiple strings for that column). So, filtering on multiple columns (e.g., filter out "Pool" samples from the group column, then filtering a specific sample from the the sample column) requires running subset_targets() twice. This is also a little un-intuitive. In the pipeline, the main input to subset_targets() is the targets dataframe made by make_targets(), but the output of subset_targets() is a list, where the first element is the targets data frame. So, to filter twice, the current code is kinda awkward:

targets <- make_targets(...) filter1 <- subset_targets(targets, filter_column = "group", rm.vals = "Pool") final_targets <- subset_targets(filter1$targets, filter_column = "sample", rm.vals = c("sampleA", "sampleB")

Might be nice to change this so that you can do all the filtering at once. Maybe by filtering on a named list, where the name is the column and the list element is the stuff to get filtered, e.g.:

targets <- make_targets(...) final_targets <- subset_targets(targets, filter = list("group" = c("Pool"), "sample" = c("sampleA", "sampleB")))

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