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3.7 years ago
B- for bioinformatics
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30
Hi "trigger"'s function inferGenotype shows error in strsplit (See below).
Rstudio_Rnotebook file
```{r}
library(tigger)
library(alakazam)
library(dplyr)
```
```{r}
lung0_2 <- readChangeoDb("Z:/light_IGLK_lung0_2_parse-select.tab")
Notes: Reading mouse immunoglobulin light chain V and J region genes fasta file
ighv <-readIgFasta("Z:/imgt_mouse_IGKJ_V.fasta")
```
```{r}
colnames(lung0_2)
[1] "SEQUENCE_ID" "SEQUENCE_INPUT" "FUNCTIONAL" "IN_FRAME" "STOP" "MUTATED_INVARIANT" "INDELS" "LOCUS" "V_CALL" "D_CALL"
[11] "J_CALL" "SEQUENCE_VDJ" "SEQUENCE_IMGT" "V_SEQ_START" "V_SEQ_LENGTH" "V_GERM_START_VDJ" "V_GERM_LENGTH_VDJ" "V_GERM_START_IMGT" "V_GERM_LENGTH_IMGT" "NP1_LENGTH"
[21] "D_SEQ_START" "D_SEQ_LENGTH" "D_GERM_START" "D_GERM_LENGTH" "NP2_LENGTH" "J_SEQ_START" "J_SEQ_LENGTH" "J_GERM_START" "J_GERM_LENGTH" "JUNCTION"
[31] "JUNCTION_LENGTH" "GERMLINE_IMGT" "V_SCORE" "V_IDENTITY" "V_EVALUE" "V_CIGAR" "D_SCORE" "D_IDENTITY" "D_EVALUE" "D_CIGAR"
[41] "J_SCORE" "J_IDENTITY" "J_EVALUE" "J_CIGAR" "FWR1_IMGT" "FWR2_IMGT" "FWR3_IMGT" "FWR4_IMGT" "CDR1_IMGT" "CDR2_IMGT"
[51] "CDR3_IMGT" "CELL" "C_CALL" "CONSCOUNT" "UMICOUNT" "V_CALL_10X" "D_CALL_10X" "J_CALL_10X" "JUNCTION_10X" "JUNCTION_10X_AA"
```{r}
nv <- findNovelAlleles(lung0_2, ighv, v_call = "V_CALL", j_call = "J_CALL", seq = "SEQUENCE_IMGT", junction = "JUNCTION", junction_length = "JUNCTION_LENGTH", germline_min = 10, min_seqs = 10, auto_mutrange = TRUE, mut_range = 1:10, pos_range = 1:312, y_intercept = 0.125, alpha = 0.05, j_max = 0.15, min_frac = 0.75, nproc = 1)
selectNovel(nv) %>% select(germline_call, polymorphism_call)
```
```{r}
gt <- inferGenotype(lung0_2, germline_db=ighv, novel=nv)
```
**Traceback**
**Error in strsplit(., ",") : non-character argument**
10.strsplit(., ",")
9.function_list[[i]](value)
8.reduce(value, `_function_list`)
7.`_fseq`(`_lhs`)
6.eval(quote(`_fseq`(`_lhs`)), env, env)
5.eval(quote(`_fseq`(`_lhs`)), env, env)
4.withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
3.allele_calls %>% strsplit(",") %>% unlist %>% setdiff(names(germline_db))
2.findUnmutatedCalls(allele_calls, as.character(data[[seq]]), germline_db)
1.inferGenotype(lung0_2, germline_db = ighv, novel = nv)