Off topic:gene names for ballgown

Question

[mo.ghasemi717]

Hi recently I performed an analysis on my data using stringtie and ballgown but i cant find my gene names, these are my commands:

    setwd("E:/share2/ball2")
    setRepositories
    library(ballgown)
    library(genefilter)
    library(dbplyr)
    library(magrittr)
    library(dplyr)
    library(readxl)
    remotes::install_github("alyssafrazee/RSkittleBrewer",force = TRUE)
pheno_data = read_excel("E:/my meta data.xlsx",col_names = T)
pheno_data<-as.data.frame(pheno_data)
bg_chrX = ballgown(dataDir = "ballgown", pData = pheno_data,samples = dir)
bg_chrX_filt = subset(bg_chrX,"rowVars(texpr(bg_chrX)) >1",genomesubset=TRUE)
results_transcripts <-stattest(bg_chrX_filt, feature='transcript', covariate='sex' 
          , getFC=TRUE, meas='FPKM')
results_transcripts <- data.frame(geneNames = ballgown::geneNames(bg_chrX_filt),
                                  geneIDs = ballgown::geneIDs(bg_chrX_filt),
                                  results_transcripts)

as you see in the result there is no even one gene name, look this:

    geneNames  geneIDs    feature  id        fc      pval      qval
9           .  MSTRG.2 transcript   9 0.8954503 0.5568966 0.9975262
40          .  MSTRG.2 transcript  40 1.0819969 0.7945403 0.9986724
50          . MSTRG.38 transcript  50 0.9637638 0.8832754 0.9986724
100         . MSTRG.50 transcript 100 1.1624027 0.4955879 0.9975262
101         . MSTRG.51 transcript 101 1.1214982 0.7252486 0.9985385
102         . MSTRG.52 transcript 102 0.7734894 0.2886172 0.9975262

is there any problem in commands?? how can I find my gene names directly??