ChromVAR data uploading

Renfang2019 commented 5 years ago

peaks <- getPeaks(peakfile, sort_peaks = TRUE) Warning: 2388 parsing failures. row col expected actual file 129030 X1 a double X '/Users/mac4/Desktop/ChromVAR/E16WTc_nPN_peaks.narrowPeak' 129031 X1 a double X '/Users/mac4/Desktop/ChromVAR/E16WTc_nPN_peaks.narrowPeak' 129032 X1 a double X '/Users/mac4/Desktop/ChromVAR/E16WTc_nPN_peaks.narrowPeak' 129033 X1 a double X '/Users/mac4/Desktop/ChromVAR/E16WTc_nPN_peaks.narrowPeak' 129034 X1 a double X '/Users/mac4/Desktop/ChromVAR/E16WTc_nPN_peaks.narrowPeak' ...... ... ........ ...... .......................................................... See problems(...) for more details.

Error in seqlevels[rankSeqlevels(seqlevels)] <- seqlevels : NAs are not allowed in subscripted assignments Can you please help with the data reading?

AliciaSchep commented 5 years ago

I suspect this has to do with how the chromosome are encoded, that they are '1' '2' etc but then it is getting an unexpected type when it reads 'X'. Either change the formatting in the input or use an alternate method for reading in peaks (e.g. if you call read_csv directly for initial reading, you can specify the column types)

Renfang2019 commented 5 years ago

Thank you very much Alicia. we add chr into the narrowpeak file and sam file, but it showed us the same message. I checked the trouble shooting with the peak reading add the x with 10000 but it did run for me since it said could not find the file.

Is it possible I share one set of our narrowpeak and sam file with you so you can try it and see what we need to change for our file? We have been trying for three days and almost gave up. If you could help, that would be great!

Thank you so much.

Have a wonderful day.

Renfang

Dr. Renfang Song Taylor Assistant Professor Department of Biology College of Science and Mathematics SOUTHWEST BAPTIST UNIVERSITY 1600 University Ave. | Bolivar MO 65613 Room: Wheeler Science Center 114D OFFICE 417.328.1669 rtaylor@SBUniv.edumailto:cmarsch@SBUniv.edu Follow us: Facebookhttps://www.facebook.com/SBUniv | Twitterhttp://www.twitter.com/SBUniv | Instagram[cid:a808aec3-70ce-4651-b432-8f78c2cd0ee6]http://www.instagram.com/sbuniv

Proverbs 2:10-11.For wisdom will enter your heart, and knowledge will be pleasant to your soul. and understanding will guard you. 箴言2：10-11智慧必入你心．你的靈要以知識為美 . 謀略必護衛你．聰明必保守你

From: Alicia Schep notifications@github.com Sent: Wednesday, June 19, 2019 3:10 PM To: GreenleafLab/chromVAR Cc: Renfang Taylor; Author Subject: Re: [GreenleafLab/chromVAR] ChromVAR data uploading (#56)

I suspect this has to do with how the chromosome are encoded, that they are '1' '2' etc but then it is getting an unexpected type when it reads 'X'. Either change the formatting in the input or use an alternate method for reading in peaks (e.g. if you call read_csv directly for initial reading, you can specify the column types)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/GreenleafLab/chromVAR/issues/56?email_source=notifications&email_token=AMMOBOTLUBCKN5DFJQJFRYLP3LYMFA5CNFSM4HZBABXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYD35IA#issuecomment-503824032, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMMOBOQLSGIIKC6565F2WKDP3LYMFANCNFSM4HZBABXA.

AliciaSchep commented 5 years ago

It looks like your file is narrowPeak format? Have you tried readNarrowpeaks ? (still might need the chromosome change to have 'chr', that is a bug #37 )

Renfang2019 commented 5 years ago

Thank you. I add chr and it showed me this error after I tried to center the peaks:

resize(peaks,width = 300,fix = "center") GRanges object with 131417 ranges and 0 metadata columns: seqnames ranges strand
[1] chr1 3116858-3117157 * [2] chr1 3117302-3117601 * [3] chr1 3360973-3361272 * [4] chr1 3372658-3372957 * [5] chr1 3395523-3395822 * ... ... ... ... [131413] chrY 90804897-90805196 * [131414] chrY 90807486-90807785 * [131415] chrY 90808695-90808994 * [131416] chrY 90812359-90812658 * [131417] chrY 90812712-90813011 * ------- seqinfo: 21 sequences from an unspecified genome; no seqlengths

What could it be the problems? I was reading other issues and found out it needs two samples, how do I combine the two narrowpeak files or do I input the two narrowpeak files separately? Thank you so much! Have a great day.

Renfang2019 commented 5 years ago

I just tried readnarrowpeaks, it shows me this: same error in seqinfo:21 sequences from an unspecified genome;no seqlengths. What should I do, please please help! Thank you very much!

peakfile <- readNarrowpeaks("E16WTc_nPN_peakschr.narrowPeak") Parsed with column specification: cols( chr = col_character(), start = col_double(), end = col_double(), name = col_character(), score = col_double(), strand = col_character(), fc = col_double(), pval = col_double(), qval = col_double(), summit = col_double() ) peaks <- getPeaks(peakfile,sort_peaks = TRUE) Error: file must be a string, raw vector or a connection. resize(peaks,width = 300,fix = "center") GRanges object with 131417 ranges and 0 metadata columns: seqnames ranges strand
[1] chr1 3116858-3117157 * [2] chr1 3117302-3117601 * [3] chr1 3360973-3361272 * [4] chr1 3372658-3372957 * [5] chr1 3395523-3395822 * ... ... ... ... [131413] chrY 90804897-90805196 * [131414] chrY 90807486-90807785 * [131415] chrY 90808695-90808994 * [131416] chrY 90812359-90812658 * [131417] chrY 90812712-90813011 * ------- seqinfo: 21 sequences from an unspecified genome; no seqlengths

GreenleafLab / chromVAR

ChromVAR data uploading #56