Processing a list in chunks and combining the result

问题

I have two lists of gene-lists for example

gene_list_A

$`STEARATE BIOSYNTHESIS I (ANIMALS)%HUMANCYC%PWY-5972`
 [1] "ELOVL1"  "ACOT7"   "ACSL1"   "ACSL5"   "ACSL4"   "ELOVL6"  "ACSL3"   "ACOT2"   "ACOT1"   "ACSBG1" 
[11] "ACSBG2"  "SLC27A2" "ACOT4"  

$`SUPERPATHWAY OF INOSITOL PHOSPHATE COMPOUNDS%HUMANCYC%PWY-6371`
 [1] "PI4K2B"  "MTMR14"  "PTEN"    "INPPL1"  "PIK3CD"  "PIK3C2G" "PIK3CB"  "PIK3C2A" "PIK3CG"  "PIK3C2B"
[11] "PLCZ1"   "PPIP5K1" "PPIP5K2" "PIP5KL1" "PLCE1"   "PIP4K2A" "PIP4K2B" "PIP4K2C" "SACM1L"  "ITPK1"  
[21] "IPMK"    "OCRL"    "ITPKB"   "MINPP1"  "ITPKC"   "PLCB3"   "PLCB4"   "PIK3CA"  "ITPKA"   "PIK3C3" 
[31] "PLCB1"   "PLCB2"   "PI4K2A"  "TMEM55A" "IPPK"    "TMEM55B" "MTMR3"   "PIK3R4"  "PIK3R3"  "PIK3R2" 
[41] "PIK3R1"  "PIK3R6"  "PIK3R5"  "INPP5B"  "INPP5A"  "INPP5D"  "INPP5J"  "PLCG2"   "PIP5K1A" "INPP5K" 
[51] "PIP5K1B" "PLCG1"   "PIP5K1C" "IP6K1"   "CDIPT"   "IP6K3"   "IP6K2"   "SYNJ2"   "FIG4"    "PIKFYVE"
[61] "SYNJ1"   "PLCH1"   "PLCH2"   "PI4KB"   "PLCD3"   "PLCD4"   "PLCD1"

gene_list_B
$bupropion
 [1] "CHRNA1"  "CHRNA3"  "CHRNA4"  "CHRNB1"  "CHRNB2"  "CHRNB4"  "CHRND"   "CHRNG"   "CYP2C19" "SLC6A2" 
[11] "SLC6A3" 

$dopamine
 [1] "ADRA2A"   "APEX1"    "CA1"      "CA12"     "CA14"     "CA2"      "CA3"      "CA4"      "CA5A"    
[10] "CA5B"     "CA6"      "CA7"      "CA9"      "DRD1"     "DRD2"     "DRD3"     "DRD4"     "EHMT2"   
[19] "FEN1"     "HIF1A"    "HSD17B10" "KDM4E"    "MPHOSPH8" "MTNR1A"   "MTNR1B"   "NFE2L2"   "RECQL"   
[28] "SLC6A2"   "SLC6A3"   "TDP1"     "TP53"

The lists are large

> length(gene_list_A) 
[1] 10362
> length(gene_list_B)
[1] 5145

I process the two lists through the following functions

gs.RNASeq <- 21196
gom.obj <- newGOM(gene_list_A,gene_list_B,gs.RNASeq)
Intersection <- getMatrix(gom.obj, name="pval")

These lines of code work fine when the length of the gene list is small but crashes when the length is large. As in this case length(gene_list_A) = 10362 and length(gene_list_B) = 5145

As a hack, I want to process this in chunks of gene_list_B (and gene_list_A remains constant)

this is my script which I wrote using this thread.

Intersection <- as.data.frame(matrix(NA,nrow = length(gene_list_A), ncol = length(gene_list_B)))

nSym <- length(gene_list_B)
chunkSize <- 10
for(i in 1:ceiling(nSym / chunkSize)){
  Intersection[,] <- getMatrix(newGOM(gene_list_A,gene_list_B[((i-1)*chunkSize+1):min(nSym,(i*chunkSize))],gs.RNASeq),name= "pval")
  }

dim(Intersection)

The script runs but has a lot of errors

I am not sure if I am calling and filling "Intersection" the empty data frame correctly in the script.
If I run a small list as a test run the answer with and without hack are different.

Can anyone please help me in solving this? The script I have written may be wrong so any other changes, suggestions also welcome

Thanks

来源：https://stackoverflow.com/questions/63984981/processing-a-list-in-chunks-and-combining-the-result

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list

loops