ADAL01

Listing of Anti-Drug Antibody Data for Patients with At Least One ADA Sample Datum by Treatment

Output

Standard Listing
Data Setup

Preview
Try this using WebR

Code

lsting <- as_listing(
  out,
  key_cols = c("USUBJID", "VISIT"),
  disp_cols = names(out),
  main_title = paste0(
    "Listing of Anti-", drugcd, " Antibody Data for Patients with At Least One ADA Sample Datum by Treatment, ",
    "PK Population\nProtocol: ", drug_a
  ),
  subtitles = paste("\nTreatment Group:", trt),
  main_footer = "(1) Minimum reportable titer = 1.10 (example only)
(2) Minimum reportable titer = 1.10 (example only)
(3) Minimum reportable concentration = 3.0 (example only)
BLQ = Below Limit of Quantitation, LTR = Lower than Reportable, N/A = Not Applicable, N.C. = Not Calculable,
ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies)
ROXXXXXXX is also known as [drug]"
)

tail(lsting, 50)[1:24, ]

Listing of Anti-R1800000 Antibody Data for Patients with At Least One ADA Sample Datum by Treatment, PK Population
Protocol: A: Drug X Antibody

Treatment Group: A: Drug X

———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                       ADA     NAb                  Sample        Patient        Patient                   
                                            Nominal   Titer   Titer    Sample    Neutralizing    Treatment      Treatment         Drug     
                                             Time     Units   Units     ADA        Antibody     Emergent ADA   Emergent NAb   Concentration
     Subject ID         Visit   Timepoint    (hr)      (1)     (2)     Result    (NAb) Result      Status         Status       (ug/mL) (3) 
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
AB12345-PAK-11-id-145   Day 1    Predose     0.00      N/A     N/A    Negative     Negative       Negative       Negative          N/A     
                        Day 2      24H       1.00      N/A     N/A    Negative     Negative                                        N/A     
AB12345-PAK-11-id-187   Day 1    Predose     0.00      N/A     N/A    Negative     Negative       Positive       Negative          N/A     
                        Day 2      24H       1.00     1.16    1.16    Positive     Positive                                        N/A     
AB12345-PAK-11-id-268   Day 1    Predose     0.00      N/A     N/A    Negative     Negative       Negative       Negative          N/A     
                        Day 2      24H       1.00      N/A     N/A    Negative     Negative                                        N/A     
AB12345-PAK-11-id-68    Day 1    Predose     0.00     1.08    1.08    Positive     Positive       Positive       Negative          N/A     
                        Day 2      24H       1.00     1.19    1.19    Positive     Positive                                        N/A     
AB12345-PAK-12-id-328   Day 1    Predose     0.00     1.11    1.11    Positive     Positive       Negative       Negative          N/A     
                        Day 2      24H       1.00      N/A     N/A    Negative     Negative                                        N/A     
AB12345-PAK-12-id-85    Day 1    Predose     0.00     1.06    1.06    Positive     Positive       Positive       Negative          N/A     
                        Day 2      24H       1.00     1.35    1.35    Positive     Positive                                        N/A     
AB12345-PAK-13-id-251   Day 1    Predose     0.00      N/A     N/A    Negative     Negative       Positive       Negative          N/A     
                        Day 2      24H       1.00     1.14    1.14    Positive     Positive                                        N/A     
AB12345-PAK-14-id-117   Day 1    Predose     0.00     1.04    1.04    Positive     Positive       Positive       Negative          N/A     
                        Day 2      24H       1.00     1.06    1.06    Positive     Positive                                        N/A     
AB12345-PAK-15-id-314   Day 1    Predose     0.00      N/A     N/A    Negative     Negative       Positive       Negative          N/A     
                        Day 2      24H       1.00     1.02    1.02    Positive     Positive                                        N/A     
AB12345-PAK-2-id-213    Day 1    Predose     0.00     1.24    1.24    Positive     Positive       Negative       Negative          N/A     
                        Day 2      24H       1.00      N/A     N/A    Negative     Negative                                        N/A     
 AB12345-RUS-1-id-52    Day 1    Predose     0.00      N/A     N/A    Negative     Negative       Positive       Negative          N/A     
                        Day 2      24H       1.00     1.22    1.22    Positive     Positive                                        N/A     
AB12345-RUS-13-id-70    Day 1    Predose     0.00      N/A     N/A    Negative     Negative       Negative       Negative          N/A     
                        Day 2      24H       1.00      N/A     N/A    Negative     Negative                                        N/A     
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

(1) Minimum reportable titer = 1.10 (example only)
(2) Minimum reportable titer = 1.10 (example only)
(3) Minimum reportable concentration = 3.0 (example only)
BLQ = Below Limit of Quantitation, LTR = Lower than Reportable, N/A = Not Applicable, N.C. = Not Calculable,
ADA = Anti-Drug Antibodies (is also referred to as ATA, or Anti-Therapeutic Antibodies)
ROXXXXXXX is also known as [drug]

Experimental use!

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Code

library(dplyr)
library(rlistings)
library(random.cdisc.data)

adpc <- cadpc
adab <- cadab

trt <- "A: Drug X"
min_titer_ada <- 1.10
min_titer_nab <- 1.10
min_conc <- 3.0

if (unique(adpc$RELTMU) == "hr") adpc$NFRLT <- adpc$NFRLT / 24
adpc_f <- adpc %>% filter(PARAM == "Plasma Drug X")


drug_a <- unique(adab$PARCAT1)[1]
drugcd <- unique(adab$PARAMCD[adab$PARAM == "Antibody titer units"])[1]
conc_u <- unique(adpc_f$AVALU)

adpc_f <- adpc_f %>% select(USUBJID, NFRLT, AVAL)
adab1 <- adab %>%
  filter(ARM == trt) %>%
  select(-PARAM, -PARCAT1, -AVALC, -AVALU) %>%
  left_join(
    adpc_f,
    by = c("USUBJID", "NFRLT"),
    suffix = c("_ab", "_pk")
  ) %>%
  filter(!is.na(AVAL_ab))

adab_f <- adab1 %>%
  tidyr::pivot_wider(
    id_cols = c(USUBJID, VISIT, NFRLT, ISTPT, AVAL_pk),
    names_from = PARAMCD,
    values_from = AVAL_ab
  )
# Select the necessary ADA parameters
adab_f1 <- adab_f %>%
  select(USUBJID, VISIT, NFRLT, ISTPT, AVAL_pk, R1800000, R1800001, RESULT1, RESULT2, ADASTAT1, ADASTAT2) %>%
  mutate(ADA = R1800000, NAB = R1800001) %>%
  select(-R1800000, -R1800001)


# Find subject level ADA status
adab_s <- adab_f1 %>%
  select(USUBJID, ADASTAT1, ADASTAT2) %>%
  filter(!is.na(ADASTAT1), !is.na(ADASTAT2))
# Find time-vary ADA records
adab_r <- adab_f1 %>%
  select(-ADASTAT1, -ADASTAT2) %>%
  filter(!is.na(VISIT))

adab_o <- adab_r %>% left_join(adab_s, by = "USUBJID")

out <- adab_o %>%
  mutate(AVAL_pk = ifelse(AVAL_pk == 0, NA, AVAL_pk)) %>%
  mutate(NFRLT = as.numeric(NFRLT)) %>%
  mutate(
    RESULT1 = ifelse(RESULT1 == 1, "Positive", "Negative"),
    RESULT2 = ifelse(RESULT2 == 1, "Positive", "Negative"),
    ADASTAT1 = ifelse(ADASTAT1 == 1, "Positive", "Negative"),
    ADASTAT2 = ifelse(ADASTAT2 == 1, "Positive", "Negative"),
    # ADA = ifelse(ADA < min_titer_ada, NA, ADA),
    # NAB = ifelse(NAB < min_titer_nab, NA, NAB),
    AVAL_pk = ifelse(AVAL_pk < min_conc, "BLQ", AVAL_pk)
  ) %>%
  select(
    USUBJID, VISIT, ISTPT, NFRLT, ADA, NAB, RESULT1, RESULT2, ADASTAT1, ADASTAT2,
    AVAL_pk
  ) %>%
  mutate_at(
    c("NFRLT", "ADA", "NAB", "AVAL_pk"),
    ~ ifelse(is.na(.), replace(., is.na(.), "N/A"), format(round(., 2), nsmall = 2))
  )

var_labels(out) <- names(out)

out <- out %>%
  arrange(USUBJID, VISIT, desc(ISTPT), NFRLT) %>%
  group_by(USUBJID) %>%
  mutate(
    ADASTAT1 = ifelse(row_number() == 1, ADASTAT1, ""),
    ADASTAT2 = ifelse(row_number() == 1, ADASTAT2, "")
  ) %>% # Keep only the first value in ADA status, set others to ""
  var_relabel(
    USUBJID = "Subject ID",
    VISIT = "Visit",
    ISTPT = "Timepoint",
    NFRLT = "Nominal\nTime\n(hr)",
    RESULT1 = "Sample\nADA\nResult",
    ADA = "ADA\nTiter\nUnits\n(1)",
    ADASTAT1 = "Patient\nTreatment\nEmergent ADA\nStatus",
    RESULT2 = "Sample\nNeutralizing\nAntibody\n(NAb) Result",
    NAB = "NAb\nTiter\nUnits\n(2)",
    ADASTAT2 = "Patient\nTreatment\nEmergent NAb\nStatus",
    AVAL_pk = paste0("Drug\nConcentration\n(", conc_u, ") (3)")
  )

Reproducibility

Timestamp

[1] "2024-11-20 09:53:19 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2024-11-20
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version date (UTC) lib source
 backports           1.5.0   2024-05-23 [1] RSPM
 brio                1.1.5   2024-04-24 [1] RSPM
 checkmate           2.3.2   2024-07-29 [1] RSPM
 cli                 3.6.3   2024-06-21 [1] RSPM
 codetools           0.2-20  2024-03-31 [2] CRAN (R 4.4.1)
 curl                6.0.1   2024-11-14 [1] RSPM
 digest              0.6.37  2024-08-19 [1] RSPM
 dplyr             * 1.1.4   2023-11-17 [1] RSPM
 evaluate            1.0.1   2024-10-10 [1] RSPM
 fansi               1.0.6   2023-12-08 [1] RSPM
 fastmap             1.2.0   2024-05-15 [1] RSPM
 formatters        * 0.5.9   2024-09-12 [1] RSPM
 generics            0.1.3   2022-07-05 [1] RSPM
 glue                1.8.0   2024-09-30 [1] RSPM
 htmltools           0.5.8.1 2024-04-04 [1] RSPM
 htmlwidgets         1.6.4   2023-12-06 [1] RSPM
 jsonlite            1.8.9   2024-09-20 [1] RSPM
 knitr               1.49    2024-11-08 [1] RSPM
 lifecycle           1.0.4   2023-11-07 [1] RSPM
 magrittr            2.0.3   2022-03-30 [1] RSPM
 pillar              1.9.0   2023-03-22 [1] RSPM
 pkgcache            2.2.3   2024-09-12 [1] RSPM
 pkgconfig           2.0.3   2019-09-22 [1] RSPM
 processx            3.8.4   2024-03-16 [1] RSPM
 ps                  1.8.1   2024-10-28 [1] RSPM
 purrr               1.0.2   2023-08-10 [1] RSPM
 R6                  2.5.1   2021-08-19 [1] RSPM
 random.cdisc.data * 0.3.16  2024-10-10 [1] RSPM
 rlang               1.1.4   2024-06-04 [1] RSPM
 rlistings         * 0.2.9   2024-06-20 [1] RSPM
 rmarkdown           2.29    2024-11-04 [1] RSPM
 sessioninfo         1.2.2   2021-12-06 [1] any (@1.2.2)
 stringi             1.8.4   2024-05-06 [1] RSPM
 stringr             1.5.1   2023-11-14 [1] RSPM
 testthat            3.2.1.1 2024-04-14 [1] RSPM
 tibble            * 3.2.1   2023-03-20 [1] RSPM
 tidyr               1.3.1   2024-01-24 [1] RSPM
 tidyselect          1.2.1   2024-03-11 [1] RSPM
 utf8                1.2.4   2023-10-22 [1] RSPM
 vctrs               0.6.5   2023-12-01 [1] RSPM
 withr               3.0.2   2024-10-28 [1] RSPM
 xfun                0.49    2024-10-31 [1] RSPM
 yaml                2.3.10  2024-07-26 [1] RSPM

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

──────────────────────────────────────────────────────────────────────────────

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Output

Reproducibility

Timestamp

Session Info

.lock file

`.lock` file