Entering edit mode
I am trying to use the locfunc="shorth" in the estimatesizeFactors function for DESeq2 but am getting the error that the locfunc function doesn't exist. I've only found similar errors for DESeq and those solutions don't work (median <- NULL or removing global variables). I also made sure that genefilter library was loaded since it's what is listed as connecting shorth and got the same error. Below, I list the code line that is the problem as well as the libraries I loaded. When I did not include locfunc="shorth" or manually put locfunc=stats::median, it works fine. Thank you so much in advance!
##############################
# PROBLEMATIC CODE #
library(seqgendiff)
library(data.table)
library(stringr)
library(ggplot2)
library(DESeq2)
library(genefilter)
dds_bid_2rep_1000ft_rat_shorth = estimateSizeFactors(dds_bid_2rep_1000ft, type="ratio", locfunc="shorth")
# OUTPUT #
Error in locfunc((log(cnts) - loggeomeans)[is.finite(loggeomeans) & cnts > : could not find function "locfunc"
Traceback:
1. estimateSizeFactors(dds_bid_2rep_1000ft, type = "ratio", locfunc = "shorth")
2. estimateSizeFactors(dds_bid_2rep_1000ft, type = "ratio", locfunc = "shorth")
3. .local(object, ...)
4. estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,
. geoMeans = geoMeans, controlGenes = controlGenes)
5. apply(counts, 2, function(cnts) {
. exp(locfunc((log(cnts) - loggeomeans)[is.finite(loggeomeans) &
. cnts > 0]))
. })
6. FUN(newX[, i], ...)
################################
# WHEN TRY TO FIND FUNCTION #
library(sos)
findFn("locfunc") has output "found 0 matches"
?locfunc & ??locfunc can't find anything
# please also include the results of running the following in an R session
sessionInfo( )
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS/LAPACK: /Users/hopekirby/miniconda3/envs/r-kernel/lib/libopenblasp-r0.3.23.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Denver
tzcode source: system (macOS)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] genefilter_1.82.1 DESeq2_1.40.2
[3] SummarizedExperiment_1.30.2 Biobase_2.60.0
[5] MatrixGenerics_1.12.2 matrixStats_1.0.0
[7] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1
[9] IRanges_2.34.1 S4Vectors_0.38.1
[11] BiocGenerics_0.46.0 cowplot_1.1.1
[13] ggplot2_3.4.3 stringr_1.5.0
[15] data.table_1.14.8 seqgendiff_1.2.3
loaded via a namespace (and not attached):
[1] KEGGREST_1.40.0 gtable_0.3.4 lattice_0.21-8
[4] vctrs_0.6.3 tools_4.3.0 bitops_1.0-7
[7] generics_0.1.3 parallel_4.3.0 RSQLite_2.3.1
[10] AnnotationDbi_1.62.2 tibble_3.2.1 fansi_1.0.4
[13] blob_1.2.4 pkgconfig_2.0.3 Matrix_1.5-4.1
[16] assertthat_0.2.1 uuid_1.1-0 lifecycle_1.0.3
[19] GenomeInfoDbData_1.2.10 compiler_4.3.0 Biostrings_2.68.1
[22] munsell_0.5.0 repr_1.1.6 codetools_0.2-19
[25] htmltools_0.5.5 RCurl_1.98-1.12 pillar_1.9.0
[28] crayon_1.5.2 BiocParallel_1.34.2 cachem_1.0.8
[31] DelayedArray_0.26.7 abind_1.4-5 tidyselect_1.2.0
[34] locfit_1.5-9.8 digest_0.6.33 stringi_1.7.12
[37] dplyr_1.1.2 splines_4.3.0 fastmap_1.1.1
[40] grid_4.3.0 colorspace_2.1-0 cli_3.6.1
[43] magrittr_2.0.3 S4Arrays_1.0.5 base64enc_0.1-3
[46] survival_3.5-5 XML_3.99-0.14 utf8_1.2.3
[49] IRdisplay_1.1 withr_2.5.0 scales_1.2.1
[52] bit64_4.0.5 IRkernel_1.3.2 XVector_0.40.0
[55] httr_1.4.6 bit_4.0.5 pbdZMQ_0.3-9
[58] png_0.1-8 memoise_2.0.1 evaluate_0.21
[61] rlang_1.1.1 Rcpp_1.0.11 DBI_1.1.3
[64] xtable_1.8-4 glue_1.6.2 annotate_1.78.0
[67] jsonlite_1.8.7 R6_2.5.1 zlibbioc_1.46.0
