locfunc not found in DESeq2
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Entering edit mode
Hope ▴ 10
@993cf259
Last seen 4 weeks ago
United States

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
locfunc DESeq2 shorth estimateSizeFactors • 280 views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 3 days ago
United States

The argument for locfunc is meant to be a function, not a character vector. You should instead use locfunc = genefilter::shorth.

1
Entering edit mode
Hope ▴ 10
@993cf259
Last seen 4 weeks ago
United States

Thank you James! Here's an example of how the function should be implemented if others get confused haha. The locfunc is a variable that you assign to a FUNCTION. Therefore, if you want to use shorth, you use the function shorth (or genefilter::shorth) NOT a string "shorth". Example implementation of my code is below:

dds_bid_2rep_1000ft_rat_shorth = estimateSizeFactors(dds_bid_2rep_1000ft, type="ratio", locfunc=genefilter::shorth)
OR
dds_bid_2rep_1000ft_rat_shorth = estimateSizeFactors(dds_bid_2rep_1000ft, type="ratio", locfunc=shorth)
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