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    CyrielleHoluka
    @CyrielleHoluka
    Thank you !
    Aurélien Ginolhac
    @ginolhac
    in case of trouble, focus on vroom. It will load all files at once and guess correctly the delimiter
    12 replies
    image.png
    Aurélien Ginolhac
    @ginolhac
    reaching this is one command once the pcr_files is correct. Extracting the sample and replicate is more difficult and require 2 steps.
    • extract the "mlc\\d_\\d" info
    • use separate() afterwards
    RubensBegaj
    @RubensBegaj
    hjjbjkvb
    Show in New WindowClear OutputExpand/Collapse Output
    Errore: 'C:/Users/rubens.begaj/Documents/PhD/Courses/2020/Data processing with R tidyverse _26 November/Practical/data/pcr/data/pcr/.csv' does not exist.
    5.
    stop("'", path, "' does not exist", if (!is_absolute_path(path)) { paste0(" in current working directory ('", getwd(), "')") }, ".", call. = FALSE)
    4.
    checkpath(path)
    3.
    (function (path, write = FALSE) { if (is.raw(path)) { return(rawConnection(path, "rb")) ...
    2.
    vroom
    (file, delim = delim %||% col_types$delim, col_names = col_names, col_types = col_types, id = id, skip = skip, col_select = col_select, name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws, escape_double = escape_double, escape_backslash = escape_backslash, ...
    1.
    vroom(here::here("data", "pcr", "
    .csv"))
    I am in the right folder and set it as currently working directorydirectory
    26 replies
    Kostaskotz
    @Kostaskotz
    ok for my PCR files I have the command pcr_files <- dir(here::here("data", "pcr"), full.names = FALSE), but what i get is not what you got ( I am not sure how to make r markdown to show the message liek you do) All i get is a file with jsut the PCR files name not the path
    17 replies
    Aurélien Ginolhac
    @ginolhac
    once pcr_files is correct, vroom(pcr_files, id = "file") does the job
    Andreas Jahnen
    @andreasjahnen
    When do we need to send our "results"? 13:30?
    1 reply
    Kostaskotz
    @Kostaskotz
    image.png
    1 reply
    this is how my pcr_data looks
    CyrielleHoluka
    @CyrielleHoluka
    pcr_files <- dir(here::here("Data", "data", "pcr"), full.names = TRUE) : this is my code for Pcr files but the outcome is not good at all, can someone help me please ?
    19 replies
    Maxime Sunnen
    @MaximeSunnen_twitter
    The resulting tibble indicates "NA" for the new sample column? pcr_data_vroom %>%
    mutate(sample= str_extract(file, "mlc1\d.csv"),
    replicate=strextract(file, "(?<=)\d"))
    8 replies
    sorry, wrong copy paste.
    pcr_data_vroom %>%
    mutate(sample= str_extract(file, "mlc1\d"),
    replicate=strextract(file, "(?<=)\d"))
    15 replies
    Screenshot 2020-11-30 at 12.48.03.png
    8 replies
    RubensBegaj
    @RubensBegaj
    Immagine 2020-11-30 125013.png
    1 reply
    Maxime Sunnen
    @MaximeSunnen_twitter
    Screenshot 2020-11-30 at 12.53.26.png
    Roland Krause
    @rolandkrause
    OK, so I will take over now for Aurélien again. A few tips:
    1. You can use basic markdown here. If you put words between backticks, they are rendered as code.
    2. Don't share screenshots of code.
    3. You need to conclude by 13:30 but we will accept partial answers depending on documented effort. Put in comments to show what you wanted.
    RubensBegaj
    @RubensBegaj
    ????
    Roland Krause
    @rolandkrause
    1. Please reply in threads, that helps.
    CyrielleHoluka
    @CyrielleHoluka
    image.png
    This is my table is it ok ?
    CyrielleHoluka
    @CyrielleHoluka
    purrr:: map_dfr(pcr_files, dplyr:: bind_rows()) : I got this message Can't convert a tbl_df/tbl/data.frame object to function
    Roland Krause
    @rolandkrause
    No need to run run bind_rows(), that's used internally.
    CyrielleHoluka
    @CyrielleHoluka
    So I don't need to do it ?
    Roland Krause
    @rolandkrause
    It looks as if you have the data read in, so no.
    CyrielleHoluka
    @CyrielleHoluka
    Because I got a nice table so I don't understand for what it is
    Oh ok thank you, I'll go to the next question
    Roland Krause
    @rolandkrause
    I think quite a few of you will need a bit more time and deserve a break. So please send until 13:30 but we will continue at 14:00.
    Kostaskotz
    @Kostaskotz
    Where do we send ?
    4 replies
    CyrielleHoluka
    @CyrielleHoluka
    I have some trouble to create pcr_data_vroom : pcr_data_vroom<-vroom(here::here("Data", "data", "pcr", files, id= "file")),
    I am not sure it can recognized all my files
    7 replies
    MZizovic
    @mickypz
    When do we restart the session?
    A ok, at 14h
    Roland Krause
    @rolandkrause
    Here is a spreadsheet with assignments of participants to projects. https://docs.google.com/spreadsheets/d/1I5nuP7gu8Nt18Bh2XV0TH7KbSr6hwEPAsJQdSE7gLXU/edit?usp=sharing
    Sorry, wrong link
    Roland Krause
    @rolandkrause
    I hope...
    Aurélien Ginolhac
    @ginolhac
    Program at 9.30 am:
    • What's new in the tidyverse in 2020 (~ 20 minutes)
    • Presentation of targets and how the website is generated (~ 10 minutes)
    Roland Krause
    @rolandkrause
    image.png
    Updated just now.
    Roland Krause
    @rolandkrause
    10:30 - ms-transform
    11:00 - dicom-json
    11:30 - otu-pivot
    12:00 - bachelor students
    12:30 - rna-seq
    13:00 Lunch break
    EleftheriaCha
    @EleftheriaCha
    http://www.riffomonas.org/code_club/ free online tutorials and excersises I found quite helpful
    Corrado Ameli
    @CorradoAmeliLU
    How do we submit the project?
    Roland Krause
    @rolandkrause
    By mail to Aurelien and me.
    LynnMangen
    @LynnMangen
    where do we find the link to enter the webex
    vero1166
    @vero1166
    Roland will share with you on the project-related room
    Roland Krause
    @rolandkrause
    Dear all, thank you for your participation over the last days. Please fill the feedback forms https://j.mp/37AgAzx !
    Roland Krause
    @rolandkrause
    The lectures have all been uploaded to the ownCloud share.