saveToGTF: saves dataframes to cufflinks specific GTF format
In psikon/cuffgo: cufflinks and GO analysis

Description Usage Arguments Format References Examples

This wrapper function creates from a dataframe processed in R an GTF File in cufflinks specific GTF format. There will be different fields in GTF Files for every program of the cufflinks suite, so you have to choose the right program to save your data.

1 2	saveToGTF(filename, program = "cufflinks", dataframe)

`filename`	path to the save location
`program`	for which program the GTF File will be created (default="cufflinks")
`dataframe`	saves this dataframe

All three programs have 8 standard tab delimited values that have to be provided by every programm and a variable attribute field that is separated by semicolons. this attribute field is different between all three programs. Standard fields:

chr: Chromosome or contig name
program: The name of the program that generated this file
feature: The type of record (always either "transcript" or "exon"
start: The leftmost coordinate of this record
end: The rightmost coordinate of this record
score: The most abundant isoform for each gene is assigned a score of 1000. Minor isoforms are scored by the ratio (minor FPKM/major FPKM)
strand: Cufflinks' guess for which strand the isoform came from. Always one of "+", "-", "."
frame: deprecated - field not used

cufflinks specific attributes:

gene_id: Cufflinks gene id
transcript_id: Cufflinks transcript id
exon_number: number of exon for this transcript
fpkm: Isoform-level relative abundance in Fragments Per Kilobase of exon model per Million mapped fragment
frac: deprecated value
conf_lo: Lower bound of the 95% confidence interval of the abundance of this isoform, as a fraction of the isoform abundance. That is, lower bound = FPKM * (1.0 - conf_lo)
conf_hi: Upper bound of the 95% confidence interval of the abundance of this isoform, as a fraction of the isoform abundance. That is, upper bound = FPKM * (1.0 + conf_lo)
cov: Estimate for the absolute depth of read coverage across the whole transcript
full_read_support: When RABT assembly is used, this attribute reports whether or not all introns and internal exons were fully covered by reads from the data.

cuffcompare specific attributes:

gene_id: Cufflinks gene id
transcript_id: Cufflinks transcript id
exon_number: number of exon for this transcript
gene_name: The gene_name attribute of the reference GTF record for this transcript, if present. Otherwise gene_id is used.
oId: old identifier of this gene e.g. in cufflinks output
nearest_ref: The reference transcript to which the class code refers, if any
class_code: The type of relationship between the Cufflinks transcripts and the reference transcript
tss_id: The tss_id associated with the object, or "-" if not a transcript/primary transcript, or if tss_id isn't present

cuffmerge specific attributes:

gene_id: Cufflinks gene id
transcript_id: Cufflinks transcript id
exon_number: number of exon for this transcript
gene_name: The gene_name attribute of the reference GTF record for this transcript, if present. Otherwise gene_id is used.
oId: old identifier of this gene e.g. in cufflinks output
contained_in: is this transcript contained in a nother bigger transcript
nearest_ref: The reference transcript to which the class code refers, if any
class_code: The type of relationship between the Cufflinks transcripts and the reference transcript
tss_id: The tss_id associated with the object, or "-" if not a transcript/primary transcript, or if tss_id isn't present

CUfflinks Manual: http://cufflinks.cbcb.umd.edu/manual.html

         ## save cufflinks GTF File
         saveToGTF("test.gtf", "cufflinks", cufflinks)
         
         ## save cuffmerge GTF File
         saveToGTF("test.gtf", "cuffmerge", cuffmerge)
      
         ##save cuffcompare GTF File
         saveToGTF("test.gtf", "cuffcompare",cuffcompare)