magrittr pipe to righthand side in braces gives error - r

Question

I am using the magrittr pipe %>% to pipe an object into multiple arguments in the righthand side function, using curly braces to force :
data_bec <- dds_tmp %>%
{sva::ComBat_seq(
counts = . %>% SummarizedExperiment::assay(),
batch = . %>% magrittr::extract2("batch") %>% droplevels(),
covar_mod = cbind(
time = . %>% magrittr::extract2("time") %>% droplevels(),
treatment = . %>% magrittr::extract2("treatment") %>% droplevels()
)
)}
Which gives this error:
Error in unique.default(x, nmax = nmax) :
unique() applies only to vectors
However, the code below works:
data_bec <- dds_tmp %>%
{sva::ComBat_seq(
counts = SummarizedExperiment::assay(.),
batch = magrittr::extract2(., "batch") %>% droplevels(),
covar_mod = cbind(
time = magrittr::extract2(., "time") %>% droplevels(),
treatment = magrittr::extract2(., "treatment") %>% droplevels()
)
)}
I can't wrap my head around why magrittr::extract2(., "batch") %>% droplevels() works inside a function inside braces, but . %>% magrittr::extract2("batch") %>% droplevels() doesn't work. Is there an easy way to understand this behavior?
NB: My dds_tmp object is large and produced by DESeq2::sample_table. Here is a small example data set:
dds_tmp <- new(
"DESeqDataSet",
design = ~ 1,
dispersionFunction = function ()
NULL,
rowRanges = new(
"CompressedGRangesList",
unlistData = new(
"GRanges",
seqnames = new(
"Rle",
values = structure(integer(0), .Label = character(0), class = "factor"),
lengths = integer(0),
elementMetadata = NULL,
metadata = list()
),
ranges = new(
"IRanges",
start = integer(0),
width = integer(0),
NAMES = NULL,
elementType = "ANY",
elementMetadata = NULL,
metadata = list()
),
strand = new(
"Rle",
values = structure(integer(0), .Label = c("+",
"-", "*"), class = "factor"),
lengths = integer(0),
elementMetadata = NULL,
metadata = list()
),
seqinfo = new(
"Seqinfo",
seqnames = character(0),
seqlengths = integer(0),
is_circular = logical(0),
genome = character(0)
),
elementMetadata = new(
"DFrame",
rownames = NULL,
nrows = 0L,
listData = structure(list(), .Names = character(0)),
elementType = "ANY",
elementMetadata = NULL,
metadata = list()
),
elementType = "ANY",
metadata = list()
),
elementMetadata = new(
"DFrame",
rownames = NULL,
nrows = 50L,
listData = structure(list(), .Names = character(0)),
elementType = "ANY",
elementMetadata = new(
"DFrame",
rownames = NULL,
nrows = 0L,
listData = list(type = character(0), description = character(0)),
elementType = "ANY",
elementMetadata = NULL,
metadata = list()
),
metadata = list()
),
elementType = "GRanges",
metadata = list(),
partitioning = new(
"PartitioningByEnd",
end = c(
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L
),
NAMES = c(
"0610005C13Rik", "0610007C21Rik", "0610007L01Rik", "0610007N19Rik",
"0610007P08Rik", "0610007P14Rik", "0610007P22Rik", "0610008F07Rik",
"0610009B14Rik", "0610009B22Rik", "0610009D07Rik", "0610009L18Rik",
"0610009O20Rik", "0610010B08Rik", "0610010F05Rik", "0610010K14Rik",
"0610010O12Rik", "0610011F06Rik", "0610011L14Rik", "0610012G03Rik",
"0610012H03Rik", "0610030E20Rik", "0610031J06Rik", "0610031O16Rik",
"0610037L13Rik", "0610037P05Rik", "0610038B21Rik", "0610038L08Rik",
"0610039K10Rik", "0610040B10Rik", "0610040F04Rik", "0610040J01Rik",
"0610043K17Rik", "0910001L09Rik", "100043387", "1100001G20Rik",
"1110001A16Rik", "1110001J03Rik", "1110002B05Rik", "1110002L01Rik",
"1110002N22Rik", "1110003E01Rik", "1110004E09Rik", "1110004F10Rik",
"1110005A03Rik", "1110006O24Rik", "1110007C09Rik", "1110008F13Rik",
"1110008J03Rik", "1110008L16Rik"
),
elementType = "ANY",
elementMetadata = NULL,
metadata = list()
)
),
colData = new(
"DFrame",
rownames = c(
"IM_MR30_S30_L001", "IM_MR31_S31_L001", "IM_MR32_S32_L001",
"IM_MR33_S33_L001", "IM_MR34_S34_L001", "IM_MR35_S35_L001",
"IM_MR36_S36_L001", "IM_AR_30", "IM_AR_31", "IM_AR_32", "IM_AR_33"
),
nrows = 11L,
listData = list(
batch = structure(
c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L),
.Label = c(
"190701_K00242_0579_AH7GFLBBXY",
"180810_K00242_0453_AHVJTJBBXX-IM-AR-RS21+180814_K00242_0456_AHW5LYBBXX-IM-AR-RS21+180817_K00242_0458_AHW57TBBXX-IM-AR-RS21",
"180406_K00242_0385_AHTCCHBBXX-IM-AR-RS8+180412_K00242_0388_AHT7NYBBXX-IM-AR-RS8",
"180814_K00242_0456_AHW5LYBBXX-IM-AR-RS21+180814_K00242_0456_AHW5LYBBXX-IM-AR-RS21+180817_K00242_0458_AHW57TBBXX-IM-AR-RS21",
"190322_K00242_0534_AHYLVWBBXX_IM-AM-RS8-dT"
),
class = "factor"
),
time_label = c( "D8", "D10", "D10", "D10", "D15", "D15", "D15", "D6",
"D6", "D6", "D6"
),
time_value = c(8L, 10L,
10L, 10L, 15L, 15L, 15L, 6L, 6L, 6L, 6L),
user = c("MR",
"MR", "MR", "MR", "MR", "MR", "MR", "AR", "AR", "AR",
"AR"),
treatment = structure(
c(1L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 1L),
.Label = c("ctrl", "OE"),
class = "factor"
),
group = structure(
c(10L, 11L, 11L, 11L, 12L, 12L, 12L,
13L, 13L, 13L, 14L),
.Label = c(
"M_2i_ctrl", "M_D0_ctrl", "M_D1_ctrl", "M_D2_ctrl", "M_D3_ctrl",
"M_D4_ctrl", "M_D5_ctrl", "M_D6_ctrl", "M_D7_ctrl", "M_D8_ctrl",
"M_D10_ctrl", "M_D15_ctrl", "A_D6_OE", "A_D6_ctrl", "A_D7_ctrl",
"A_D7_OE", "A_D8_ctrl", "A_D8_OE", "A_D11_ctrl", "A_D11_OE"
),
class = "factor"
),
group_pca_label = c(
NA, "M_D10_ctrl", NA, NA, "M_D15_ctrl", NA, NA, "A_D6_OE", NA, NA,
"A_D6_ctrl"
),
condition = structure(
c(10L,
11L, 11L, 11L, 13L, 13L, 13L, 14L, 14L, 14L, 8L),
.Label = c(
"2i_ctrl", "D0_ctrl", "D1_ctrl", "D2_ctrl", "D3_ctrl", "D4_ctrl",
"D5_ctrl", "D6_ctrl", "D7_ctrl", "D8_ctrl", "D10_ctrl", "D11_ctrl",
"D15_ctrl", "D6_OE", "D7_OE", "D8_OE", "D11_OE"
),
class = "factor"
),
time = structure(
c(10L, 11L, 11L,
11L, 13L, 13L, 13L, 8L, 8L, 8L, 8L),
.Label = c(
"2i", "D0", "D1", "D2", "D3", "D4", "D5", "D6", "D7", "D8", "D10",
"D11", "D15"
),
class = "factor"
)
),
elementType = "ANY",
elementMetadata = new(
"DFrame",
rownames = NULL,
nrows = 9L,
listData = list(
type = c(
"input", "input", "input", "input", "input", "input", "input",
"input", "input"
),
description = c("",
"", "", "", "", "", "", "", "")
),
elementType = "ANY",
elementMetadata = NULL,
metadata = list()
),
metadata = list()
),
assays = new(
"SimpleAssays",
data = new(
"SimpleList",
listData = list(counts = structure(
c(
0L, 221L, 582L, 60L, 392L, 521L, 88L, 0L, 0L, 99L, 405L, 3L, 345L,
0L, 221L, 151L, 4L, 63L, 227L, 117L, 11L, 376L, 406L, 0L, 143L,
255L, 5L, 0L, 0L, 7L, 5L, 1L, 0L, 182L, 8L, 0L, 87L, 20L, 381L, 71L,
58L, 331L, 56L, 589L, 36L, 2L, 73L, 254L, 55L, 95L, 0L, 381L, 691L,
80L, 353L, 397L, 126L, 0L, 0L, 151L, 434L, 6L, 374L, 0L, 242L, 134L,
43L, 113L, 232L, 130L, 23L, 325L, 458L, 0L, 165L, 358L, 4L, 0L, 0L,
10L, 0L, 0L, 4L, 225L, 7L, 0L, 100L, 52L, 486L, 115L, 73L, 512L,
86L, 639L, 50L, 3L, 108L, 273L, 64L, 105L, 0L, 261L, 588L, 65L,
334L, 367L, 88L, 0L, 0L, 102L, 389L, 8L, 333L, 0L, 216L, 158L, 38L,
87L, 254L, 87L, 24L, 302L, 434L, 0L, 159L, 292L, 4L, 0L, 2L, 7L, 1L,
1L, 0L, 197L, 12L, 0L, 86L, 39L, 482L, 99L, 58L, 408L, 67L, 657L,
43L, 1L, 73L, 242L, 63L, 68L, 0L, 271L, 579L, 88L, 298L, 383L, 80L,
0L, 0L, 95L, 358L, 3L, 271L, 0L, 195L, 143L, 23L, 64L, 200L, 82L,
27L, 334L, 382L, 0L, 170L, 296L, 4L, 0L, 0L, 4L, 0L, 1L, 1L, 171L,
14L, 0L, 122L, 26L, 365L, 86L, 62L, 343L, 67L, 589L, 35L, 1L, 59L,
251L, 39L, 71L, 0L, 332L, 566L, 112L, 330L, 282L, 82L, 0L, 0L, 107L,
318L, 1L, 349L, 0L, 218L, 119L, 122L, 68L, 143L, 111L, 26L, 413L,
540L, 0L, 124L, 315L, 0L, 0L, 1L, 6L, 0L, 1L, 3L, 235L, 13L, 0L,
88L, 66L, 508L, 99L, 71L, 510L, 73L, 532L, 46L, 1L, 145L, 342L, 49L,
60L, 0L, 297L, 598L, 100L, 283L, 278L, 58L, 0L, 0L, 115L, 306L, 4L,
368L, 0L, 208L, 109L, 105L, 81L, 190L, 113L, 13L, 406L, 563L, 0L,
115L, 280L, 5L, 0L, 0L, 4L, 0L, 1L, 2L, 238L, 22L, 0L, 78L, 75L,
532L, 54L, 53L, 484L, 79L, 510L, 35L, 1L, 154L, 361L, 46L, 45L, 0L,
413L, 724L, 102L, 352L, 325L, 77L, 0L, 0L, 87L, 364L, 8L, 398L, 0L,
201L, 130L, 94L, 63L, 227L, 116L, 16L, 398L, 594L, 0L, 127L, 312L,
4L, 0L, 0L, 8L, 0L, 0L, 0L, 285L, 12L, 0L, 99L, 61L, 638L, 56L, 44L,
562L, 80L, 604L, 32L, 3L, 178L, 394L, 51L, 81L, 0L, 342L, 1147L,
136L, 887L, 568L, 197L, 0L, 0L, 192L, 644L, 13L, 653L, 0L, 601L,
286L, 36L, 98L, 478L, 190L, 8L, 706L, 694L, 0L, 229L, 306L, 11L, 0L,
1L, 9L, 0L, 6L, 10L, 221L, 39L, 0L, 132L, 109L, 1132L, 350L, 133L,
567L, 115L, 931L, 61L, 5L, 70L, 561L, 130L, 133L, 0L, 337L, 1162L,
135L, 927L, 578L, 182L, 0L, 0L, 242L, 665L, 21L, 702L, 0L, 674L,
307L, 35L, 122L, 475L, 176L, 8L, 653L, 714L, 0L, 251L, 312L, 11L,
0L, 3L, 15L, 0L, 9L, 10L, 209L, 31L, 0L, 168L, 111L, 1231L, 383L,
150L, 552L, 129L, 980L, 72L, 4L, 52L, 686L, 142L, 130L, 1L, 284L,
1159L, 145L, 861L, 529L, 168L, 0L, 0L, 202L, 688L, 3L, 670L, 0L,
654L, 298L, 27L, 122L, 465L, 197L, 15L, 707L, 657L, 0L, 223L, 284L,
6L, 0L, 1L, 13L, 0L, 3L, 10L, 199L, 31L, 0L, 125L, 88L, 1142L, 397L,
121L, 593L, 128L, 888L, 60L, 7L, 54L, 595L, 117L, 150L, 0L, 224L,
1228L, 68L, 894L, 674L, 213L, 0L, 0L, 197L, 798L, 12L, 758L, 0L,
446L, 285L, 21L, 75L, 458L, 185L, 5L, 738L, 456L, 0L, 261L, 339L,
7L, 0L, 0L, 9L, 0L, 0L, 1L, 180L, 32L, 0L, 110L, 98L, 919L, 249L,
134L, 387L, 188L, 1055L, 64L, 3L, 52L, 630L, 110L, 175L
),
.Dim = c(50L, 11L),
.Dimnames = list(
c(
"0610005C13Rik", "0610007C21Rik", "0610007L01Rik",
"0610007N19Rik", "0610007P08Rik", "0610007P14Rik",
"0610007P22Rik", "0610008F07Rik", "0610009B14Rik",
"0610009B22Rik", "0610009D07Rik", "0610009L18Rik",
"0610009O20Rik", "0610010B08Rik", "0610010F05Rik",
"0610010K14Rik", "0610010O12Rik", "0610011F06Rik",
"0610011L14Rik", "0610012G03Rik", "0610012H03Rik",
"0610030E20Rik", "0610031J06Rik", "0610031O16Rik",
"0610037L13Rik", "0610037P05Rik", "0610038B21Rik",
"0610038L08Rik", "0610039K10Rik", "0610040B10Rik",
"0610040F04Rik", "0610040J01Rik", "0610043K17Rik",
"0910001L09Rik", "100043387", "1100001G20Rik", "1110001A16Rik",
"1110001J03Rik", "1110002B05Rik", "1110002L01Rik",
"1110002N22Rik", "1110003E01Rik", "1110004E09Rik",
"1110004F10Rik", "1110005A03Rik", "1110006O24Rik",
"1110007C09Rik", "1110008F13Rik", "1110008J03Rik", "1110008L16Rik"
),
c(
"IM_MR30_S30_L001", "IM_MR31_S31_L001", "IM_MR32_S32_L001",
"IM_MR33_S33_L001", "IM_MR34_S34_L001", "IM_MR35_S35_L001",
"IM_MR36_S36_L001", "IM_AR_30", "IM_AR_31", "IM_AR_32", "IM_AR_33"
)
)
)),
elementType = "ANY",
elementMetadata = NULL,
metadata = list()
)
),
NAMES = NULL,
elementMetadata = new(
"DFrame",
rownames = NULL,
nrows = 50L,
listData = structure(list(), .Names = character(0)),
elementType = "ANY",
elementMetadata = NULL,
metadata = list()
),
metadata = list(version = structure(
list(c(1L, 30L, 1L)), class = c("package_version",
"numeric_version")
))
)

Answer 1

We can use
data_bec <- dds_tmp %>%
{sva::ComBat_seq(
counts = {.} %>% SummarizedExperiment::assay(),
batch = {.} %>% magrittr::extract2("batch") %>% droplevels(),
covar_mod = cbind(
time = {.} %>% magrittr::extract2("time") %>% droplevels(),
treatment = {.} %>% magrittr::extract2("treatment") %>% droplevels()
)
)}