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add messaging #262

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merged 3 commits into from
Nov 22, 2022
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add messaging #262

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add messaging
stemangiola Nov 14, 2022
58e52fe
add messaging
stemangiola Nov 14, 2022
5cb798c
Merge branch 'improve-DE-docs' of github.com:stemangiola/tidybulk int…
stemangiola Nov 14, 2022
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22 changes: 22 additions & 0 deletions R/functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -472,6 +472,28 @@ get_differential_transcript_abundance_bulk <- function(.data,
)
)

# Specify the design column tested
if(is.null(.contrasts))
message(
sprintf(
"tidybulk says: The design column being tested is %s",
design %>% colnames %>% .[1]
)
)

# If I don't have intercept or I have categorical factor of interest BUT I don't have contrasts
if(
is.null(.contrasts) &
(
(
! .data |> pull(parse_formula(.formula)[1]) |> is("numeric") &
.data |> pull(parse_formula(.formula)[1]) |> unique() |> length() |> gt(2)
) |
colnames(design)[1] != "(Intercept)"
)
)
warning("tidybulk says: If you have (i) an intercept-free design (i.e. ~ 0 + factor) or you have a categorical factor of interest with more than 2 values you should use the `contrasts` argument.")

my_contrasts =
.contrasts %>%
ifelse_pipe(length(.) > 0,
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