GETWITHINGENEEXPRESSION(1)

💖 GETWITHINGENEEXPRESSION(1) — the girlies' guide 💖

okay so bestie, welcome to getWithinGeneExpression, section 1 of the manual 🎀 she's a little command-line icon and she's here to compute the relative expression of transcripts within genes. that's it, that's the whole girl. let's get into it ✨

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🌸 NAME 🌸

getWithinGeneExpression — compute relative expression of transcripts within genes 💅

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✨ SYNOPSIS ✨

getWithinGeneExpression -t <trInfoFileName>  [OPTIONS] [samplesFile]

like. -t is non-negotiable, she's the main character 👑 everything else is optional and [samplesFile] is just vibing at the end there.

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🦋 DESCRIPTION 🦋

So what does she actually do? Computes relative expression of transcripts within genes. periodt. 🌸

And now the important bit, so pay attention bestie:

• [samplesFile] should contain transposed MCMC expression samples. noted. transposed. do not come to her with untransposed samples, she will not know what to do with them 😭
• the program can produce means and variance and write them into [sumFile], or it can give you the individual MCMC samples, which get written into [outFile]. so basically: summary stats girlie, or raw samples girlie. choose your fighter 💅

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💅 OPTIONS 💅

she's got range, she's got flags. no cap.

• --help — Show this help information. the girl explains herself, we love a self-aware queen ✨
• -a, --adjustByLength — Adjust expression by transcripts length. (default: Off) so if your transcripts have wildly different lengths and you want her to care about that, flip her on 🎀
• -G <geneListFile>, --geneList=<geneListFile> — Name of the file containing list of gene names (one for each transcript). one gene name per transcript, okay? one. per. transcript. 💀
• --groupByGene — Group transcripts by genes (this can change the default order of output. (default: Off) ok listen, heads up — this can change the default order of the output, so don't come for her if the ordering shifts 🙈
• -l, --log — Use logged values. (default: Off) take the log, bestie 🌈
• -o <outFileName>, --outFile=<outFileName> — Name of the output file. where the individual MCMC samples go, iykyk 👑
• -s <sumFileName>, --sumFile=<sumFileName> — Name of summarization file where true mean, true variance, relative mean and relative variance are saved. that's four whole things in one file, she's efficient 💖
• -t <trInfoFileName>, --trInfoFile=<trInfoFileName> — Name of the transcript file. this one's required, she's the moment, don't skip her ⭐
• -T <trMapFile>, --trMap=<trMapFile> — Name of the file containing transcript to gene mapping. tell her which transcript belongs to which gene, she's not a mind reader 🧚
• --updateTrFile — Update trInfoFile if new gene names were provided (with trMapFile or geneListFile). (default: Off) so like, if you rolled up with fresh gene names, she can refresh trInfoFile for you 💅
• -v, --verbose — Verbose output. (default: Off) she'll narrate her whole life to you. honestly? iconic. 🎀

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ngl the defaults are Off for basically everything, so if you want her to do the extra cute stuff you've gotta ask. she's not gonna assume 💅

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and that's the whole page, bestie 🫶 go forth and compute. this was getWithinGeneExpression 0.7.5... from September 2021 — shoutout to the source for the lore, mwah 💖 bye babes! ✨🌸🦋