Hi, I am testing cHAMP and in the step 3 (Test data) it appear the warning: (In readLines(csvfile) : incomplete final line found on 'C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/lung_test_set.csv')
testDir=system.file("extdata",package="ChAMPdata") > myLoad <- champ.load(testDir,arraytype="450K") [===========================] [<<<< ChAMP.LOAD START >>>>>] ----------------------------- [ Loading Data with ChAMP Method ] ---------------------------------- Note that ChAMP method will NOT return rgSet or mset, they object defined by minfi. Which means, if you use ChAMP method to load data, you can not use SWAN or FunctionNormliazation method in champ.norm() (you can use BMIQ or PBC still). But All other function should not be influenced. [===========================] [<<<< ChAMP.IMPORT START >>>>>] ----------------------------- [ Section 1: Read PD Files Start ] CSV Directory: C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/lung_test_set.csv Find CSV Success Reading CSV File Replace Sentrix_Position into Array Replace Sentrix_ID into Slide [ Section 1: Read PD file Done ] [ Section 2: Read IDAT files Start ] Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7990895118_R03C02_Grn.idat ---- (1/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7990895118_R05C02_Grn.idat ---- (2/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/9247377086_R01C01_Grn.idat ---- (3/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/9247377086_R02C01_Grn.idat ---- (4/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7766130112_R06C01_Grn.idat ---- (5/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7766130112_R01C02_Grn.idat ---- (6/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7990895118_R01C01_Grn.idat ---- (7/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7990895118_R01C02_Grn.idat ---- (8/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7990895118_R03C02_Red.idat ---- (1/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7990895118_R05C02_Red.idat ---- (2/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/9247377086_R01C01_Red.idat ---- (3/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/9247377086_R02C01_Red.idat ---- (4/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7766130112_R06C01_Red.idat ---- (5/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7766130112_R01C02_Red.idat ---- (6/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7990895118_R01C01_Red.idat ---- (7/8) Loading:C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/7990895118_R01C02_Red.idat ---- (8/8) Extract Mean value for Green and Red Channel Success Your Red Green Channel contains 622399 probes. [ Section 2: Read IDAT Files Done ] [ Section 3: Use Annotation Start ] Reading 450K Annotation >> Fetching NEGATIVE ControlProbe. Totally, there are 613 control probes in Annotation. Your data set contains 613 control probes. Generating Meth and UnMeth Matrix Extracting Meth Matrix... Totally there are 485512 Meth probes in 450K Annotation. Your data set contains 485512 Meth probes. Extracting UnMeth Matrix... Totally there are 485512 UnMeth probes in 450K Annotation. Your data set contains 485512 UnMeth probes. Generating beta Matrix Generating M Matrix Generating intensity Matrix Calculating Detect P value Counting Beads [ Section 3: Use Annotation Done ] [<<<<< ChAMP.IMPORT END >>>>>>] [===========================] [You may want to process champ.filter() next.] [===========================] [<<<< ChAMP.FILTER START >>>>>] -----------------------------
In New version ChAMP, champ.filter() function has been set to do filtering on the result of champ.import(). You can use champ.import() + champ.filter() to do Data Loading, or set "method" parameter in champ.load() as "ChAMP" to get the same effect.
This function is provided for user need to do filtering on some beta (or M) matrix, which contained most filtering system in champ.load except beadcount. User need to input beta matrix, pd file themselves. If you want to do filterintg on detP matrix and Bead Count, you also need to input a detected P matrix and Bead Count information.
Note that if you want to filter more data matrix, say beta, M, intensity... please make sure they have exactly the same rownames and colnames.
[ Section 1: Check Input Start ] You have inputed beta,intensity for Analysis. pd file provided, checking if it's in accord with Data Matrix... pd file check success. Parameter filterDetP is TRUE, checking if detP in accord with Data Matrix... detP check success. Parameter filterBeads is TRUE, checking if beadcount in accord with Data Matrix... beadcount check success. parameter autoimpute is TRUE. Checking if the conditions are fulfilled... !!! ProbeCutoff is 0, which means you have no needs to do imputation. autoimpute has been reset FALSE. Checking Finished :filterDetP,filterBeads,filterMultiHit,filterSNPs,filterNoCG,filterXY would be done on beta,intensity. You also provided :detP,beadcount . [ Section 1: Check Input Done ] [ Section 2: Filtering Start >> Filtering Detect P value Start The fraction of failed positions per sample You may need to delete samples with high proportion of failed probes: Failed CpG Fraction. C1 0.0013429122 C2 0.0022162171 C3 0.0003563249 C4 0.0002842360 T1 0.0003831007 T2 0.0011946152 T3 0.0014953286 T4 0.0015447610 Filtering probes with a detection p-value above 0.01. Removing 2728 probes. If a large number of probes have been removed, ChAMP suggests you to identify potentially bad samples Filtering BeadCount Start Filtering probes with a beadcount <3 in at least 5% of samples. Removing 9291 probes Filtering NoCG Start Only Keep CpGs, removing 2959 probes from the analysis. Filtering SNPs Start Using general 450K SNP list for filtering. Filtering probes with SNPs as identified in Zhou's Nucleic Acids Research Paper 2016. Removing 57855 probes from the analysis. Filtering MultiHit Start Filtering probes that align to multiple locations as identified in Nordlund et al Removing 11 probes from the analysis. Filtering XY Start Filtering probes located on X,Y chromosome, removing 9552 probes from the analysis. Updating PD file Fixing Outliers Start Replacing all value smaller/equal to 0 with smallest positive value. Replacing all value greater/equal to 1 with largest value below 1.. [ Section 2: Filtering Done ] All filterings are Done, now you have 403116 probes and 8 samples. [<<<<< ChAMP.FILTER END >>>>>>] [===========================] [You may want to process champ.QC() next.] [<<<<< ChAMP.LOAD END >>>>>>] [===========================] [You may want to process champ.QC() next.] Warning message: In readLines(csvfile) : incomplete final line found on 'C:/Users/Asus/AppData/Local/R/win-library/4.2/ChAMPdata/extdata/lung_test_set.csv'
I appreciate if someone could help me to solve this problem. Thank you in advance. Kind regards, Luis Teves