zhengxwen
commented
3 months ago As it said, Missing characters are converted to "".
To store missing characters in GDS files, you should use SeqArray::seqAddValue() instead of add.gdsn.
See the help file of SeqArray::seqAddValue for more details.
Hi, when I want to add annotations to my gds file, I got this error. Could you help me to solve this?
Warning messages: 1: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 2: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 3: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 4: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 5: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 6: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 7: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 8: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "". 9: In add.gdsn(ans, nm[i], val[[i]], compress = compress, closezip = closezip, : Missing characters are converted to "".
My command is： Rscript 0.2.3gds2agds.R 1
and the R script is： ##########################################################################
Input
##########################################################################
gds file
dir_geno <- "/xxx/variants/rare_variant/GDS_file/" gds_file_name_1 <- "phenotype.chr" gds_file_name_2 <- ".2802.mac1.filt.gds"
annotation file (output of Annotate.R)
dir_anno <- "/xxx/variants/rare_variant/Anno/" anno_file_name_1 <- "Anno_chr" anno_file_name_2 <- "_STAARpipeline.csv"
chr <- as.numeric(commandArgs(TRUE)[1])
###########################################################################
Main Function
###########################################################################
load required package
library(gdsfmt) library(SeqArray) library(SeqVarTools) library(readr)
read annotation data
FunctionalAnnotation <- read_csv(paste0(dir_anno,"chr",chr,"/",anno_file_name_1,chr,anno_file_name_2), col_types=list(col_character(),col_double(),col_double(),col_double(),col_double(), col_double(),col_double(),col_double(),col_double(),col_double(), col_character(),col_character(),col_character(),col_double(),col_character(), col_character(),col_character(),col_character(),col_character(),col_double(), col_double(),col_character()))
dim(FunctionalAnnotation)
rename colnames
colnames(FunctionalAnnotation)[2] <- "apc_conservation" colnames(FunctionalAnnotation)[7] <- "apc_local_nucleotide_diversity" colnames(FunctionalAnnotation)[9] <- "apc_protein_function"
open GDS
gds.path <- paste0(dir_geno,gds_file_name_1,chr,gds_file_name_2) genofile <- seqOpen(gds.path, readonly = FALSE)
Anno.folder <- index.gdsn(genofile, "annotation/info") add.gdsn(Anno.folder, "FunctionalAnnotation", val=FunctionalAnnotation, compress="LZMA_ra", closezip=TRUE)
seqClose(genofile)