# Questions and answers from over the years

Sean Davis

#### Thursday, August 12, 2021

# 1 How could I generate a manifest file with filtering of Race and Ethnicity?

From https://support.bioconductor.org/p/9138939/.

    library(GenomicDataCommons,quietly = TRUE)

I made a small change to the filtering expression approach based on changes to lazy evaluation best practices. There is now no need to include the `~` in the filter expression. So:

    q = files() %>%
      GenomicDataCommons::filter(
        cases.project.project_id == 'TCGA-COAD' &
          data_type == 'Aligned Reads' &
          experimental_strategy == 'RNA-Seq' &
          data_format == 'BAM')

And get a count of the results:

    count(q)

    ## [1] 521

And the manifest.

    manifest(q)

    ## Rows: 521 Columns: 5

    ## ── Column specification ────────────────────────────────────────────────────────
    ## Delimiter: "\t"
    ## chr (4): id, filename, md5, state
    ## dbl (1): size

    ##
    ## ℹ Use `spec()` to retrieve the full column specification for this data.
    ## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Your question about race and ethnicity is a good one.

    all_fields = available_fields(files())

And we can grep for `race` or `ethnic` to get potential matching fields to look at.

    grep('race|ethnic',all_fields,value=TRUE)

    ## [1] "cases.demographic.ethnicity"
    ## [2] "cases.demographic.race"
    ## [3] "cases.follow_ups.hormonal_contraceptive_type"
    ## [4] "cases.follow_ups.hormonal_contraceptive_use"
    ## [5] "cases.follow_ups.scan_tracer_used"

Now, we can check available values for each field to determine how to complete our filter expressions.

    available_values('files',"cases.demographic.ethnicity")

    ## [1] "not hispanic or latino" "not reported"           "hispanic or latino"
    ## [4] "unknown"                "_missing"

    available_values('files',"cases.demographic.race")

    ##  [1] "white"
    ##  [2] "not reported"
    ##  [3] "black or african american"
    ##  [4] "asian"
    ##  [5] "unknown"
    ##  [6] "other"
    ##  [7] "american indian or alaska native"
    ##  [8] "native hawaiian or other pacific islander"
    ##  [9] "not allowed to collect"
    ## [10] "_missing"

We can complete our filter expression now to limit to `white` race only.

    q_white_only = q %>%
      GenomicDataCommons::filter(cases.demographic.race=='white')
    count(q_white_only)

    ## [1] 249

    manifest(q_white_only)

    ## Rows: 249 Columns: 5

    ## ── Column specification ────────────────────────────────────────────────────────
    ## Delimiter: "\t"
    ## chr (4): id, filename, md5, state
    ## dbl (1): size

    ##
    ## ℹ Use `spec()` to retrieve the full column specification for this data.
    ## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

# 2 How can I get the number of cases with RNA-Seq data added by date to TCGA project with `GenomicDataCommons`?

- From https://support.bioconductor.org/p/9135791/

I would like to get the number of cases added (created, any logical datetime would suffice here) to the TCGA project by experiment type. I attempted to get this data via GenomicDataCommons package, but it is giving me I believe the number of files for a given experiment type rather than number cases. How can I get the number of cases for which there is RNA-Seq data?

    library(tibble)
    library(dplyr)

    ##
    ## Attaching package: 'dplyr'

    ## The following objects are masked from 'package:GenomicDataCommons':
    ##
    ##     count, filter, select

    ## The following objects are masked from 'package:stats':
    ##
    ##     filter, lag

    ## The following objects are masked from 'package:base':
    ##
    ##     intersect, setdiff, setequal, union

    library(GenomicDataCommons)

    cases() %>%
      GenomicDataCommons::filter(~ project.program.name=='TCGA' &
                                   files.experimental_strategy=='RNA-Seq') %>%
      facet(c("files.created_datetime")) %>%
      aggregations() %>%
      .[[1]] %>%
      as_tibble() %>%
      dplyr::arrange(dplyr::desc(key))